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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.

rs200375319

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:45408244 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000076 (20/264690, TOPMED)
A=0.000052 (13/248886, GnomAD_exome)
A=0.000057 (8/140210, GnomAD) (+ 5 more)
A=0.000066 (8/121130, ExAC)
A=0.00020 (9/44418, ALFA)
A=0.00085 (24/28258, 14KJPN)
A=0.00060 (10/16760, 8.3KJPN)
A=0.00015 (2/13006, GO-ESP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
POLR1G : Synonymous Variant
ERCC1 : 3 Prime UTR Variant
PPP1R13L : 2KB Upstream 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 60776 G=0.99982 A=0.00018
European Sub 42734 G=0.99979 A=0.00021
African Sub 8350 G=1.0000 A=0.0000
African Others Sub 306 G=1.000 A=0.000
African American Sub 8044 G=1.0000 A=0.0000
Asian Sub 168 G=1.000 A=0.000
East Asian Sub 112 G=1.000 A=0.000
Other Asian Sub 56 G=1.00 A=0.00
Latin American 1 Sub 500 G=1.000 A=0.000
Latin American 2 Sub 628 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 8298 G=0.9998 A=0.0002


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=0.999924 A=0.000076
gnomAD - Exomes Global Study-wide 248886 G=0.999948 A=0.000052
gnomAD - Exomes European Sub 132864 G=0.999910 A=0.000090
gnomAD - Exomes Asian Sub 49008 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 34588 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 16246 G=0.99994 A=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10060 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6120 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140210 G=0.999943 A=0.000057
gnomAD - Genomes European Sub 75928 G=0.99991 A=0.00009
gnomAD - Genomes African Sub 42032 G=0.99998 A=0.00002
gnomAD - Genomes American Sub 13648 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3318 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 G=1.0000 A=0.0000
ExAC Global Study-wide 121130 G=0.999934 A=0.000066
ExAC Europe Sub 73222 G=0.99990 A=0.00010
ExAC Asian Sub 25060 G=1.00000 A=0.00000
ExAC American Sub 11570 G=1.00000 A=0.00000
ExAC African Sub 10372 G=0.99990 A=0.00010
ExAC Other Sub 906 G=1.000 A=0.000
Allele Frequency Aggregator Total Global 44418 G=0.99980 A=0.00020
Allele Frequency Aggregator European Sub 32648 G=0.99975 A=0.00025
Allele Frequency Aggregator Other Sub 6864 G=0.9999 A=0.0001
Allele Frequency Aggregator African Sub 3512 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 168 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
14KJPN JAPANESE Study-wide 28258 G=0.99915 A=0.00085
8.3KJPN JAPANESE Study-wide 16760 G=0.99940 A=0.00060
GO Exome Sequencing Project Global Study-wide 13006 G=0.99985 A=0.00015
GO Exome Sequencing Project European American Sub 8600 G=0.9999 A=0.0001
GO Exome Sequencing Project African American Sub 4406 G=0.9998 A=0.0002
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.45408244G>A
GRCh37.p13 chr 19 NC_000019.9:g.45911502G>A
ERCC1 RefSeqGene (LRG_305) NG_015839.2:g.75585C>T
Gene: ERCC1, ERCC excision repair 1, endonuclease non-catalytic subunit (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ERCC1 transcript variant 8 NM_001369412.1:c.*1431= N/A 3 Prime UTR Variant
ERCC1 transcript variant 9 NM_001369413.1:c.*1431= N/A 3 Prime UTR Variant
ERCC1 transcript variant 10 NM_001369414.1:c.*1431= N/A 3 Prime UTR Variant
ERCC1 transcript variant 11 NM_001369415.1:c.*1431= N/A 3 Prime UTR Variant
ERCC1 transcript variant 12 NM_001369416.1:c.*1431= N/A 3 Prime UTR Variant
ERCC1 transcript variant 13 NM_001369417.1:c.*1431= N/A 3 Prime UTR Variant
ERCC1 transcript variant 14 NM_001369418.1:c.*1431= N/A 3 Prime UTR Variant
ERCC1 transcript variant 15 NM_001369419.1:c.*1431= N/A 3 Prime UTR Variant
ERCC1 transcript variant 3 NM_001166049.2:c.*1431= N/A 3 Prime UTR Variant
ERCC1 transcript variant 2 NM_001983.4:c.*1431= N/A 3 Prime UTR Variant
ERCC1 transcript variant 4 NM_001369408.1:c. N/A Genic Downstream Transcript Variant
ERCC1 transcript variant 5 NM_001369409.1:c. N/A Genic Downstream Transcript Variant
ERCC1 transcript variant 6 NM_001369410.1:c. N/A Genic Downstream Transcript Variant
ERCC1 transcript variant 7 NM_001369411.1:c. N/A Genic Downstream Transcript Variant
ERCC1 transcript variant 1 NM_202001.3:c. N/A Genic Downstream Transcript Variant
Gene: PPP1R13L, protein phosphatase 1 regulatory subunit 13 like (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
PPP1R13L transcript variant 1 NM_001142502.2:c. N/A Upstream Transcript Variant
PPP1R13L transcript variant 2 NM_006663.4:c. N/A N/A
PPP1R13L transcript variant X1 XM_017026177.2:c. N/A Upstream Transcript Variant
PPP1R13L transcript variant X2 XM_017026178.2:c. N/A Upstream Transcript Variant
PPP1R13L transcript variant X3 XM_017026179.2:c. N/A Upstream Transcript Variant
Gene: POLR1G, RNA polymerase I subunit G (plus strand)
Molecule type Change Amino acid[Codon] SO Term
POLR1G transcript variant 2 NM_012099.3:c.276G>A A [GCG] > A [GCA] Coding Sequence Variant
DNA-directed RNA polymerase I subunit RPA34 isoform 2 NP_036231.1:p.Ala92= A (Ala) > A (Ala) Synonymous Variant
POLR1G transcript variant 1 NM_001297590.3:c.282G>A A [GCG] > A [GCA] Coding Sequence Variant
DNA-directed RNA polymerase I subunit RPA34 isoform 1 NP_001284519.1:p.Ala94= A (Ala) > A (Ala) Synonymous 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= A
GRCh38.p14 chr 19 NC_000019.10:g.45408244= NC_000019.10:g.45408244G>A
GRCh37.p13 chr 19 NC_000019.9:g.45911502= NC_000019.9:g.45911502G>A
ERCC1 RefSeqGene (LRG_305) NG_015839.2:g.75585= NG_015839.2:g.75585C>T
ERCC1 transcript variant 2 NM_001983.4:c.*1431= NM_001983.4:c.*1431C>T
ERCC1 transcript variant 2 NM_001983.3:c.*1431= NM_001983.3:c.*1431C>T
ERCC1 transcript variant 3 NM_001166049.2:c.*1431= NM_001166049.2:c.*1431C>T
ERCC1 transcript variant 3 NM_001166049.1:c.*1431= NM_001166049.1:c.*1431C>T
ERCC1 transcript variant 10 NM_001369414.1:c.*1431= NM_001369414.1:c.*1431C>T
ERCC1 transcript variant 12 NM_001369416.1:c.*1431= NM_001369416.1:c.*1431C>T
ERCC1 transcript variant 9 NM_001369413.1:c.*1431= NM_001369413.1:c.*1431C>T
ERCC1 transcript variant 13 NM_001369417.1:c.*1431= NM_001369417.1:c.*1431C>T
ERCC1 transcript variant 11 NM_001369415.1:c.*1431= NM_001369415.1:c.*1431C>T
ERCC1 transcript variant 15 NM_001369419.1:c.*1431= NM_001369419.1:c.*1431C>T
ERCC1 transcript variant 8 NM_001369412.1:c.*1431= NM_001369412.1:c.*1431C>T
ERCC1 transcript variant 14 NM_001369418.1:c.*1431= NM_001369418.1:c.*1431C>T
POLR1G transcript variant 1 NM_001297590.3:c.282= NM_001297590.3:c.282G>A
POLR1G transcript variant 1 NM_001297590.2:c.282= NM_001297590.2:c.282G>A
CD3EAP transcript variant 1 NM_001297590.1:c.282= NM_001297590.1:c.282G>A
POLR1G transcript variant 2 NM_012099.3:c.276= NM_012099.3:c.276G>A
CD3EAP transcript variant 2 NM_012099.2:c.276= NM_012099.2:c.276G>A
CD3EAP transcript variant 2 NM_012099.1:c.276= NM_012099.1:c.276G>A
DNA-directed RNA polymerase I subunit RPA34 isoform 1 NP_001284519.1:p.Ala94= NP_001284519.1:p.Ala94=
DNA-directed RNA polymerase I subunit RPA34 isoform 2 NP_036231.1:p.Ala92= NP_036231.1:p.Ala92=
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#.

11 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 CLINSEQ_SNP ss491769929 May 04, 2012 (137)
2 NHLBI-ESP ss713529938 Apr 25, 2013 (138)
3 EVA_EXAC ss1693673619 Apr 01, 2015 (144)
4 HUMAN_LONGEVITY ss2226045127 Dec 20, 2016 (150)
5 GNOMAD ss2744103977 Nov 08, 2017 (151)
6 GNOMAD ss2750223162 Nov 08, 2017 (151)
7 GNOMAD ss2963377238 Nov 08, 2017 (151)
8 EVA ss3825303043 Apr 27, 2020 (154)
9 TOPMED ss5076299877 Apr 26, 2021 (155)
10 TOMMO_GENOMICS ss5227969907 Apr 26, 2021 (155)
11 TOMMO_GENOMICS ss5786671203 Oct 13, 2022 (156)
12 ExAC NC_000019.9 - 45911502 Oct 12, 2018 (152)
13 gnomAD - Genomes NC_000019.10 - 45408244 Apr 26, 2021 (155)
14 gnomAD - Exomes NC_000019.9 - 45911502 Jul 13, 2019 (153)
15 GO Exome Sequencing Project NC_000019.9 - 45911502 Oct 12, 2018 (152)
16 8.3KJPN NC_000019.9 - 45911502 Apr 26, 2021 (155)
17 14KJPN NC_000019.10 - 45408244 Oct 13, 2022 (156)
18 TopMed NC_000019.10 - 45408244 Apr 26, 2021 (155)
19 ALFA NC_000019.10 - 45408244 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
ss491769929 NC_000019.8:50603341:G:A NC_000019.10:45408243:G:A (self)
4183005, 13419678, 1759986, 85939214, ss713529938, ss1693673619, ss2744103977, ss2750223162, ss2963377238, ss3825303043, ss5227969907 NC_000019.9:45911501:G:A NC_000019.10:45408243:G:A (self)
541309912, 120508307, 291845541, 2756109933, ss2226045127, ss5076299877, ss5786671203 NC_000019.10:45408243:G:A NC_000019.10:45408243:G:A (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 rs200375319

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