Name: rs3051621
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs3051621

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:127418050-127418051 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
Alleles: delAT
Variation Type: Deletion
Frequency: delAT=0.014934 (3953/264690, TOPMED)
delAT=0.016000 (2243/140190, GnomAD)
delAT=0.02870 (811/28258, 14KJPN) (+ 12 more)
delAT=0.01539 (285/18520, ALFA)
delAT=0.02918 (489/16760, 8.3KJPN)
delAT=0.0317 (203/6404, 1000G_30x)
delAT=0.0333 (167/5008, 1000G)
delAT=0.0201 (90/4480, Estonian)
delAT=0.0218 (84/3854, ALSPAC)
delAT=0.0183 (68/3708, TWINSUK)
delAT=0.0349 (64/1832, Korea1K)
delAT=0.024 (24/998, GoNL)
delAT=0.023 (14/600, NorthernSweden)
delAT=0.047 (10/212, Vietnamese)
delAT=0.05 (2/40, GENOME_DK)

Clinical Significance: Reported in ClinVar
Gene : Consequence: MEGF10 : Intron Variant
Publications: 0 citations
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	18520	AT=0.98461	=0.01539	0.96933	0.000108	0.030562	0
European	Sub	14152	AT=0.98311	=0.01689	0.966365	0.000141	0.033493	0
African	Sub	2898	AT=0.9941	=0.0059	0.988268	0.0	0.011732	0
African Others	Sub	114	AT=1.000	=0.000	1.0	0.0	0.0	N/A
African American	Sub	2784	AT=0.9939	=0.0061	0.987787	0.0	0.012213	0
Asian	Sub	112	AT=0.955	=0.045	0.910714	0.0	0.089286	0
East Asian	Sub	86	AT=0.94	=0.06	0.883721	0.0	0.116279	0
Other Asian	Sub	26	AT=1.00	=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	146	AT=0.986	=0.014	0.972603	0.0	0.027397	0
Latin American 2	Sub	610	AT=0.990	=0.010	0.980328	0.0	0.019672	0
South Asian	Sub	98	AT=0.90	=0.10	0.795918	0.0	0.204082	0
Other	Sub	504	AT=0.988	=0.012	0.97619	0.0	0.02381	0

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	AT=0.985066	delAT=0.014934
gnomAD - Genomes	Global	Study-wide	140190	AT=0.984000	delAT=0.016000
gnomAD - Genomes	European	Sub	75912	AT=0.98060	delAT=0.01940
gnomAD - Genomes	African	Sub	42024	AT=0.99393	delAT=0.00607
gnomAD - Genomes	American	Sub	13654	AT=0.98931	delAT=0.01069
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	AT=0.9521	delAT=0.0479
gnomAD - Genomes	East Asian	Sub	3128	AT=0.9482	delAT=0.0518
gnomAD - Genomes	Other	Sub	2150	AT=0.9777	delAT=0.0223
14KJPN	JAPANESE	Study-wide	28258	AT=0.97130	delAT=0.02870
Allele Frequency Aggregator	Total	Global	18520	AT=0.98461	delAT=0.01539
Allele Frequency Aggregator	European	Sub	14152	AT=0.98311	delAT=0.01689
Allele Frequency Aggregator	African	Sub	2898	AT=0.9941	delAT=0.0059
Allele Frequency Aggregator	Latin American 2	Sub	610	AT=0.990	delAT=0.010
Allele Frequency Aggregator	Other	Sub	504	AT=0.988	delAT=0.012
Allele Frequency Aggregator	Latin American 1	Sub	146	AT=0.986	delAT=0.014
Allele Frequency Aggregator	Asian	Sub	112	AT=0.955	delAT=0.045
Allele Frequency Aggregator	South Asian	Sub	98	AT=0.90	delAT=0.10
8.3KJPN	JAPANESE	Study-wide	16760	AT=0.97082	delAT=0.02918
1000Genomes_30x	Global	Study-wide	6404	AT=0.9683	delAT=0.0317
1000Genomes_30x	African	Sub	1786	AT=0.9927	delAT=0.0073
1000Genomes_30x	Europe	Sub	1266	AT=0.9755	delAT=0.0245
1000Genomes_30x	South Asian	Sub	1202	AT=0.9185	delAT=0.0815
1000Genomes_30x	East Asian	Sub	1170	AT=0.9530	delAT=0.0470
1000Genomes_30x	American	Sub	980	AT=0.994	delAT=0.006
1000Genomes	Global	Study-wide	5008	AT=0.9667	delAT=0.0333
1000Genomes	African	Sub	1322	AT=0.9924	delAT=0.0076
1000Genomes	East Asian	Sub	1008	AT=0.9504	delAT=0.0496
1000Genomes	Europe	Sub	1006	AT=0.9771	delAT=0.0229
1000Genomes	South Asian	Sub	978	AT=0.918	delAT=0.082
1000Genomes	American	Sub	694	AT=0.994	delAT=0.006
Genetic variation in the Estonian population	Estonian	Study-wide	4480	AT=0.9799	delAT=0.0201
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	AT=0.9782	delAT=0.0218
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	AT=0.9817	delAT=0.0183
Korean Genome Project	KOREAN	Study-wide	1832	AT=0.9651	delAT=0.0349
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	AT=0.976	delAT=0.024
Northern Sweden	ACPOP	Study-wide	600	AT=0.977	delAT=0.023
A Vietnamese Genetic Variation Database	Global	Study-wide	212	AT=0.953	delAT=0.047
The Danish reference pan genome	Danish	Study-wide	40	AT=0.95	delAT=0.05

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements

Sequence name	Change
GRCh38.p14 chr 5	NC_000005.10:g.127418050_127418051del
GRCh37.p13 chr 5	NC_000005.9:g.126753742_126753743del
MEGF10 RefSeqGene	NG_032072.2:g.132287_132288del

Gene: MEGF10, multiple EGF like domains 10 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MEGF10 transcript variant 2	NM_001256545.2:c.1305+238… NM_001256545.2:c.1305+238_1305+239del	N/A	Intron Variant
MEGF10 transcript variant 3	NM_001308119.2:c.1305+238… NM_001308119.2:c.1305+238_1305+239del	N/A	Intron Variant
MEGF10 transcript variant 4	NM_001308121.2:c.1305+238… NM_001308121.2:c.1305+238_1305+239del	N/A	Intron Variant
MEGF10 transcript variant 1	NM_032446.3:c.1305+238_13… NM_032446.3:c.1305+238_1305+239del	N/A	Intron Variant
MEGF10 transcript variant X2	XM_011543694.1:c.1305+238… XM_011543694.1:c.1305+238_1305+239del	N/A	Intron Variant
MEGF10 transcript variant X1	XM_017009987.2:c.1470+238… XM_017009987.2:c.1470+238_1470+239del	N/A	Intron Variant
MEGF10 transcript variant X3	XM_017009988.2:c.165+238_… XM_017009988.2:c.165+238_165+239del	N/A	Intron Variant

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: delAT (allele ID: 660518 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000831668.1	not provided	Likely-Benign

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement	AT=	delAT
GRCh38.p14 chr 5	NC_000005.10:g.127418050_127418051=	NC_000005.10:g.127418050_127418051del
GRCh37.p13 chr 5	NC_000005.9:g.126753742_126753743=	NC_000005.9:g.126753742_126753743del
MEGF10 RefSeqGene	NG_032072.2:g.132287_132288=	NG_032072.2:g.132287_132288del
MEGF10 transcript variant 2	NM_001256545.1:c.1305+238=	NM_001256545.1:c.1305+238_1305+239del
MEGF10 transcript variant 2	NM_001256545.2:c.1305+238=	NM_001256545.2:c.1305+238_1305+239del
MEGF10 transcript variant 3	NM_001308119.2:c.1305+238=	NM_001308119.2:c.1305+238_1305+239del
MEGF10 transcript variant 4	NM_001308121.2:c.1305+238=	NM_001308121.2:c.1305+238_1305+239del
MEGF10 transcript variant 1	NM_032446.2:c.1305+238=	NM_032446.2:c.1305+238_1305+239del
MEGF10 transcript variant 1	NM_032446.3:c.1305+238=	NM_032446.3:c.1305+238_1305+239del
MEGF10 transcript variant X1	XM_005272114.1:c.1305+238=	XM_005272114.1:c.1305+238_1305+239del
MEGF10 transcript variant X2	XM_005272115.1:c.1305+238=	XM_005272115.1:c.1305+238_1305+239del
MEGF10 transcript variant X2	XM_011543694.1:c.1305+238=	XM_011543694.1:c.1305+238_1305+239del
MEGF10 transcript variant X1	XM_017009987.2:c.1470+238=	XM_017009987.2:c.1470+238_1470+239del
MEGF10 transcript variant X3	XM_017009988.2:c.165+238=	XM_017009988.2:c.165+238_165+239del

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

32 SubSNP, 15 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss4282853	Jan 05, 2002 (102)
2	1000GENOMES	ss326717777	May 09, 2011 (135)
3	1000GENOMES	ss499265166	May 04, 2012 (137)
4	LUNTER	ss551542357	Apr 25, 2013 (138)
5	LUNTER	ss553216388	Apr 25, 2013 (138)
6	SSMP	ss663558663	Apr 01, 2015 (144)
7	EVA-GONL	ss982098509	Aug 21, 2014 (142)
8	1000GENOMES	ss1374463684	Aug 21, 2014 (142)
9	EVA_GENOME_DK	ss1576606612	Apr 01, 2015 (144)
10	EVA_DECODE	ss1591624058	Apr 01, 2015 (144)
11	EVA_UK10K_TWINSUK	ss1704861656	Apr 01, 2015 (144)
12	EVA_UK10K_ALSPAC	ss1704861689	Apr 01, 2015 (144)
13	JJLAB	ss2030713572	Sep 14, 2016 (149)
14	SYSTEMSBIOZJU	ss2626131086	Nov 08, 2017 (151)
15	GNOMAD	ss2830463764	Nov 08, 2017 (151)
16	SWEGEN	ss2997752540	Nov 08, 2017 (151)
17	EGCUT_WGS	ss3665662444	Jul 13, 2019 (153)
18	EVA_DECODE	ss3715652817	Jul 13, 2019 (153)
19	ACPOP	ss3732796916	Jul 13, 2019 (153)
20	KHV_HUMAN_GENOMES	ss3807205838	Jul 13, 2019 (153)
21	KOGIC	ss3957598154	Apr 26, 2020 (154)
22	TOPMED	ss4677761971	Apr 26, 2021 (155)
23	TOMMO_GENOMICS	ss5174021091	Apr 26, 2021 (155)
24	1000G_HIGH_COVERAGE	ss5265751667	Oct 13, 2022 (156)
25	HUGCELL_USP	ss5463729201	Oct 13, 2022 (156)
26	1000G_HIGH_COVERAGE	ss5550350197	Oct 13, 2022 (156)
27	SANFORD_IMAGENETICS	ss5638832973	Oct 13, 2022 (156)
28	TOMMO_GENOMICS	ss5711061686	Oct 13, 2022 (156)
29	YY_MCH	ss5806746192	Oct 13, 2022 (156)
30	EVA	ss5835608467	Oct 13, 2022 (156)
31	EVA	ss5896214813	Oct 13, 2022 (156)
32	EVA	ss5967295025	Oct 13, 2022 (156)
33	1000Genomes	NC_000005.9 - 126753742	Oct 12, 2018 (152)
34	1000Genomes_30x	NC_000005.10 - 127418050	Oct 13, 2022 (156)
35	The Avon Longitudinal Study of Parents and Children	NC_000005.9 - 126753742	Oct 12, 2018 (152)
36	Genetic variation in the Estonian population	NC_000005.9 - 126753742	Oct 12, 2018 (152)
37	The Danish reference pan genome	NC_000005.9 - 126753742	Apr 26, 2020 (154)
38	gnomAD - Genomes	NC_000005.10 - 127418050	Apr 26, 2021 (155)
39	Genome of the Netherlands Release 5	NC_000005.9 - 126753742	Apr 26, 2020 (154)
40	Korean Genome Project	NC_000005.10 - 127418050	Apr 26, 2020 (154)
41	Northern Sweden	NC_000005.9 - 126753742	Jul 13, 2019 (153)
42	8.3KJPN	NC_000005.9 - 126753742	Apr 26, 2021 (155)
43	14KJPN	NC_000005.10 - 127418050	Oct 13, 2022 (156)
44	TopMed	NC_000005.10 - 127418050	Apr 26, 2021 (155)
45	UK 10K study - Twins	NC_000005.9 - 126753742	Oct 12, 2018 (152)
46	A Vietnamese Genetic Variation Database	NC_000005.9 - 126753742	Jul 13, 2019 (153)
47	ALFA	NC_000005.10 - 127418050	Apr 26, 2021 (155)
48	ClinVar	RCV000831668.1	Apr 26, 2020 (154)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID	History Updated (Build)
rs34182766	May 23, 2006 (127)
rs144508351	Sep 17, 2011 (135)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss326717777, ss551542357, ss553216388, ss1591624058	NC_000005.8:126781640:AT:	NC_000005.10:127418049:AT:	(self)
28787186, 16010355, 11400692, 1026596, 7118154, 6081781, 31990398, 16010355, 3552936, ss499265166, ss663558663, ss982098509, ss1374463684, ss1576606612, ss1704861656, ss1704861689, ss2030713572, ss2626131086, ss2830463764, ss2997752540, ss3665662444, ss3732796916, ss5174021091, ss5638832973, ss5835608467, ss5967295025	NC_000005.9:126753741:AT:	NC_000005.10:127418049:AT:	(self)
RCV000831668.1, 37876132, 203588898, 13976155, 44898790, 515139528, 14410029040, ss3715652817, ss3807205838, ss3957598154, ss4677761971, ss5265751667, ss5463729201, ss5550350197, ss5711061686, ss5806746192, ss5896214813	NC_000005.10:127418049:AT:	NC_000005.10:127418049:AT:	(self)
ss4282853	NT_034772.6:35067613:AT:	NC_000005.10:127418049:AT:	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs3051621

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

Genomic regions, transcripts, and products
Top▲ Help
NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs3051621