Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

dbSNP Short Genetic Variations

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.

rs538772813

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:10293070 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000042 (11/264690, TOPMED)
T=0.000037 (9/243580, GnomAD_exome)
T=0.000050 (7/140280, GnomAD) (+ 4 more)
T=0.000060 (7/115816, ExAC)
T=0.00009 (4/44274, ALFA)
T=0.0003 (2/6404, 1000G_30x)
T=0.0002 (1/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ICAM5 : Missense 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 44274 G=0.99991 T=0.00009
European Sub 32538 G=0.99988 T=0.00012
African Sub 3512 G=1.0000 T=0.0000
African Others Sub 122 G=1.000 T=0.000
African American Sub 3390 G=1.0000 T=0.0000
Asian Sub 168 G=1.000 T=0.000
East Asian Sub 112 G=1.000 T=0.000
Other Asian Sub 56 G=1.00 T=0.00
Latin American 1 Sub 496 G=1.000 T=0.000
Latin American 2 Sub 628 G=1.000 T=0.000
South Asian Sub 98 G=1.00 T=0.00
Other Sub 6834 G=1.0000 T=0.0000


Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 G=0.999958 T=0.000042
gnomAD - Exomes Global Study-wide 243580 G=0.999963 T=0.000037
gnomAD - Exomes European Sub 129258 G=0.999938 T=0.000062
gnomAD - Exomes Asian Sub 48634 G=0.99998 T=0.00002
gnomAD - Exomes American Sub 34326 G=1.00000 T=0.00000
gnomAD - Exomes African Sub 15440 G=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 9918 G=1.0000 T=0.0000
gnomAD - Exomes Other Sub 6004 G=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 140280 G=0.999950 T=0.000050
gnomAD - Genomes European Sub 75940 G=0.99993 T=0.00007
gnomAD - Genomes African Sub 42064 G=1.00000 T=0.00000
gnomAD - Genomes American Sub 13664 G=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.9994 T=0.0006
gnomAD - Genomes East Asian Sub 3134 G=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 G=1.0000 T=0.0000
ExAC Global Study-wide 115816 G=0.999940 T=0.000060
ExAC Europe Sub 69584 G=0.99990 T=0.00010
ExAC Asian Sub 24656 G=1.00000 T=0.00000
ExAC American Sub 11434 G=1.00000 T=0.00000
ExAC African Sub 9294 G=1.0000 T=0.0000
ExAC Other Sub 848 G=1.000 T=0.000
Allele Frequency Aggregator Total Global 44274 G=0.99991 T=0.00009
Allele Frequency Aggregator European Sub 32538 G=0.99988 T=0.00012
Allele Frequency Aggregator Other Sub 6834 G=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 3512 G=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 G=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 496 G=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 168 G=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 T=0.00
1000Genomes_30x Global Study-wide 6404 G=0.9997 T=0.0003
1000Genomes_30x African Sub 1786 G=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 G=0.9984 T=0.0016
1000Genomes_30x South Asian Sub 1202 G=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 T=0.0000
1000Genomes_30x American Sub 980 G=1.000 T=0.000
1000Genomes Global Study-wide 5008 G=0.9998 T=0.0002
1000Genomes African Sub 1322 G=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 G=1.0000 T=0.0000
1000Genomes Europe Sub 1006 G=0.9990 T=0.0010
1000Genomes South Asian Sub 978 G=1.000 T=0.000
1000Genomes American Sub 694 G=1.000 T=0.000
Help

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.10293070G>T
GRCh37.p13 chr 19 NC_000019.9:g.10403746G>T
Gene: ICAM5, intercellular adhesion molecule 5 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ICAM5 transcript NM_003259.4:c.1289G>T R [CGC] > L [CTC] Coding Sequence Variant
intercellular adhesion molecule 5 precursor NP_003250.3:p.Arg430Leu R (Arg) > L (Leu) Missense Variant
Help

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
Help

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= T
GRCh38.p14 chr 19 NC_000019.10:g.10293070= NC_000019.10:g.10293070G>T
GRCh37.p13 chr 19 NC_000019.9:g.10403746= NC_000019.9:g.10403746G>T
ICAM5 transcript NM_003259.4:c.1289= NM_003259.4:c.1289G>T
ICAM5 transcript NM_003259.3:c.1289= NM_003259.3:c.1289G>T
intercellular adhesion molecule 5 precursor NP_003250.3:p.Arg430= NP_003250.3:p.Arg430Leu
Help

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#.

13 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1362346893 Aug 21, 2014 (142)
2 EVA_EXAC ss1693364359 Apr 01, 2015 (144)
3 HUMAN_LONGEVITY ss2224277951 Dec 20, 2016 (150)
4 GNOMAD ss2743623681 Nov 08, 2017 (151)
5 GNOMAD ss2750069430 Nov 08, 2017 (151)
6 GNOMAD ss2960445997 Nov 08, 2017 (151)
7 EVA ss3755810230 Jul 13, 2019 (153)
8 TOPMED ss5067918283 Apr 26, 2021 (155)
9 1000G_HIGH_COVERAGE ss5306489892 Oct 16, 2022 (156)
10 EVA ss5433559187 Oct 16, 2022 (156)
11 HUGCELL_USP ss5499120071 Oct 16, 2022 (156)
12 1000G_HIGH_COVERAGE ss5611886411 Oct 16, 2022 (156)
13 EVA ss5927293265 Oct 16, 2022 (156)
14 1000Genomes NC_000019.9 - 10403746 Oct 12, 2018 (152)
15 1000Genomes_30x NC_000019.10 - 10293070 Oct 16, 2022 (156)
16 ExAC NC_000019.9 - 10403746 Oct 12, 2018 (152)
17 gnomAD - Genomes NC_000019.10 - 10293070 Apr 26, 2021 (155)
18 gnomAD - Exomes NC_000019.9 - 10403746 Jul 13, 2019 (153)
19 TopMed NC_000019.10 - 10293070 Apr 26, 2021 (155)
20 ALFA NC_000019.10 - 10293070 Apr 26, 2021 (155)
Help

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
75724200, 3851651, 12937869, ss1362346893, ss1693364359, ss2743623681, ss2750069430, ss2960445997, ss3755810230, ss5433559187 NC_000019.9:10403745:G:T NC_000019.10:10293069:G:T (self)
99412346, 534028465, 283463947, 5433259556, ss2224277951, ss5067918283, ss5306489892, ss5499120071, ss5611886411, ss5927293265 NC_000019.10:10293069:G:T NC_000019.10:10293069:G:T (self)
Help

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

No publications for rs538772813

Help

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.

Software version is: 2.0.1.post761+d5e8e07