Name: rs199659954
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.

rs199659954

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:496496 (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: G>A / G>C
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.000432 (60/138910, GnomAD)
A=0.000325 (37/113824, GnomAD_exome)
A=0.00042 (35/82856, ExAC) (+ 5 more)
A=0.00000 (0/14406, ALFA)
C=0.00000 (0/14406, ALFA)
A=0.00093 (12/12934, GO-ESP)
A=0.0002 (1/6404, 1000G_30x)
A=0.0002 (1/5008, 1000G)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MADCAM1 : 5 Prime UTR 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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	30768	G=0.99961	A=0.00039, C=0.00000
European	Sub	19900	G=0.99950	A=0.00050, C=0.00000
African	Sub	7784	G=0.9999	A=0.0001, C=0.0000
African Others	Sub	298	G=1.000	A=0.000, C=0.000
African American	Sub	7486	G=0.9999	A=0.0001, C=0.0000
Asian	Sub	112	G=1.000	A=0.000, C=0.000
East Asian	Sub	86	G=1.00	A=0.00, C=0.00
Other Asian	Sub	26	G=1.00	A=0.00, C=0.00
Latin American 1	Sub	146	G=1.000	A=0.000, C=0.000
Latin American 2	Sub	610	G=1.000	A=0.000, C=0.000
South Asian	Sub	98	G=1.00	A=0.00, C=0.00
Other	Sub	2118	G=0.9995	A=0.0005, C=0.0000

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
gnomAD - Genomes	Global	Study-wide	138910	G=0.999568	A=0.000432
gnomAD - Genomes	European	Sub	75532	G=0.99935	A=0.00065
gnomAD - Genomes	African	Sub	41354	G=0.99973	A=0.00027
gnomAD - Genomes	American	Sub	13490	G=1.00000	A=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3312	G=1.0000	A=0.0000
gnomAD - Genomes	East Asian	Sub	3106	G=1.0000	A=0.0000
gnomAD - Genomes	Other	Sub	2116	G=1.0000	A=0.0000
gnomAD - Exomes	Global	Study-wide	113824	G=0.999675	A=0.000325
gnomAD - Exomes	European	Sub	76230	G=0.99955	A=0.00045
gnomAD - Exomes	Asian	Sub	15234	G=1.00000	A=0.00000
gnomAD - Exomes	American	Sub	9752	G=0.9999	A=0.0001
gnomAD - Exomes	African	Sub	9026	G=0.9998	A=0.0002
gnomAD - Exomes	Other	Sub	1882	G=1.0000	A=0.0000
gnomAD - Exomes	Ashkenazi Jewish	Sub	1700	G=1.0000	A=0.0000
ExAC	Global	Study-wide	82856	G=0.99958	A=0.00042
ExAC	Europe	Sub	53548	G=0.99938	A=0.00062
ExAC	Asian	Sub	12986	G=1.00000	A=0.00000
ExAC	American	Sub	8576	G=0.9999	A=0.0001
ExAC	African	Sub	7274	G=0.9999	A=0.0001
ExAC	Other	Sub	472	G=1.000	A=0.000
Allele Frequency Aggregator	Total	Global	14406	G=1.00000	A=0.00000, C=0.00000
Allele Frequency Aggregator	European	Sub	9810	G=1.0000	A=0.0000, C=0.0000
Allele Frequency Aggregator	African	Sub	2946	G=1.0000	A=0.0000, C=0.0000
Allele Frequency Aggregator	Other	Sub	684	G=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Latin American 2	Sub	610	G=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	G=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Asian	Sub	112	G=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=1.00	A=0.00, C=0.00
GO Exome Sequencing Project	Global	Study-wide	12934	G=0.99907	A=0.00093
GO Exome Sequencing Project	European American	Sub	8564	G=0.9989	A=0.0011
GO Exome Sequencing Project	African American	Sub	4370	G=0.9993	A=0.0007
1000Genomes_30x	Global	Study-wide	6404	G=0.9998	A=0.0002
1000Genomes_30x	African	Sub	1786	G=1.0000	A=0.0000
1000Genomes_30x	Europe	Sub	1266	G=0.9992	A=0.0008
1000Genomes_30x	South Asian	Sub	1202	G=1.0000	A=0.0000
1000Genomes_30x	East Asian	Sub	1170	G=1.0000	A=0.0000
1000Genomes_30x	American	Sub	980	G=1.000	A=0.000
1000Genomes	Global	Study-wide	5008	G=0.9998	A=0.0002
1000Genomes	African	Sub	1322	G=1.0000	A=0.0000
1000Genomes	East Asian	Sub	1008	G=1.0000	A=0.0000
1000Genomes	Europe	Sub	1006	G=0.9990	A=0.0010
1000Genomes	South Asian	Sub	978	G=1.000	A=0.000
1000Genomes	American	Sub	694	G=1.000	A=0.000

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 19	NC_000019.10:g.496496G>A
GRCh38.p14 chr 19	NC_000019.10:g.496496G>C
GRCh37.p13 chr 19	NC_000019.9:g.496496G>A
GRCh37.p13 chr 19	NC_000019.9:g.496496G>C

Gene: MADCAM1, mucosal vascular addressin cell adhesion molecule 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MADCAM1 transcript variant 1	NM_130760.3:c.-4=	N/A	5 Prime UTR Variant
MADCAM1 transcript variant 2	NM_130762.3:c.-4=	N/A	5 Prime UTR 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.

Not Reported in ClinVar

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	G=	A	C
GRCh38.p14 chr 19	NC_000019.10:g.496496=	NC_000019.10:g.496496G>A	NC_000019.10:g.496496G>C
GRCh37.p13 chr 19	NC_000019.9:g.496496=	NC_000019.9:g.496496G>A	NC_000019.9:g.496496G>C
MADCAM1 transcript variant 1	NM_130760.3:c.-4=	NM_130760.3:c.-4G>A	NM_130760.3:c.-4G>C
MADCAM1 transcript variant 1	NM_130760.2:c.-4=	NM_130760.2:c.-4G>A	NM_130760.2:c.-4G>C
MADCAM1 transcript variant 2	NM_130762.3:c.-4=	NM_130762.3:c.-4G>A	NM_130762.3:c.-4G>C
MADCAM1 transcript variant 2	NM_130762.2:c.-4=	NM_130762.2:c.-4G>A	NM_130762.2:c.-4G>C
MADCAM1 transcript variant 1	NM_130761.1:c.-4=	NM_130761.1:c.-4G>A	NM_130761.1:c.-4G>C

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#.

17 SubSNP, 9 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss489138997	May 04, 2012 (137)
2	NHLBI-ESP	ss713452876	Apr 25, 2013 (138)
3	1000GENOMES	ss1362010126	Aug 21, 2014 (142)
4	EVA_EXAC	ss1693201337	Apr 01, 2015 (144)
5	HUMAN_LONGEVITY	ss2223596908	Dec 20, 2016 (150)
6	GNOMAD	ss2743375499	Nov 08, 2017 (151)
7	GNOMAD	ss2749984173	Nov 08, 2017 (151)
8	GNOMAD	ss2959441114	Nov 08, 2017 (151)
9	EVA	ss3825203730	Apr 27, 2020 (154)
10	EVA	ss3835303696	Apr 27, 2020 (154)
11	TOPMED	ss5065160774	Apr 26, 2021 (155)
12	TOPMED	ss5065160775	Apr 26, 2021 (155)
13	EVA	ss5433010871	Oct 16, 2022 (156)
14	HUGCELL_USP	ss5498843729	Oct 16, 2022 (156)
15	1000G_HIGH_COVERAGE	ss5611434349	Oct 16, 2022 (156)
16	EVA	ss5926958319	Oct 16, 2022 (156)
17	EVA	ss5953233282	Oct 16, 2022 (156)
18	1000Genomes	NC_000019.9 - 496496	Oct 12, 2018 (152)
19	1000Genomes_30x	NC_000019.10 - 496496	Oct 16, 2022 (156)
20	ExAC	NC_000019.9 - 496496	Oct 12, 2018 (152)
21	gnomAD - Genomes	NC_000019.10 - 496496	Apr 26, 2021 (155)
22	gnomAD - Exomes	NC_000019.9 - 496496	Jul 13, 2019 (153)
23	GO Exome Sequencing Project	NC_000019.9 - 496496	Oct 12, 2018 (152)
24	TopMed Submission ignored due to conflicting rows: Row 280706438 (NC_000019.10:496495:G:A 130/264690) Row 280706439 (NC_000019.10:496495:G:C 1/264690)	-	Apr 26, 2021 (155)
25	TopMed Submission ignored due to conflicting rows: Row 280706438 (NC_000019.10:496495:G:A 130/264690) Row 280706439 (NC_000019.10:496495:G:C 1/264690)	-	Apr 26, 2021 (155)
26	ALFA	NC_000019.10 - 496496	Apr 26, 2021 (155)

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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
75374669, 3676726, 12689152, 1660738, ss489138997, ss713452876, ss1362010126, ss1693201337, ss2743375499, ss2749984173, ss2959441114, ss3825203730, ss3835303696, ss5433010871, ss5953233282	NC_000019.9:496495:G:A	NC_000019.10:496495:G:A	(self)
98960284, 531541431, 1761897315, ss2223596908, ss5065160774, ss5498843729, ss5611434349, ss5926958319	NC_000019.10:496495:G:A	NC_000019.10:496495:G:A	(self)
1761897315, ss5065160775	NC_000019.10:496495:G:C	NC_000019.10:496495:G:C	(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 rs199659954

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

rs199659954