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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 Aliases 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.

rs2316

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr19:34588527 (GRCh38.p12) 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
C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.01875 (2354/125568, TOPMED)
G=0.0183 (573/31396, GnomAD)
G=0.030 (150/5008, 1000G) (+ 5 more)
G=0.024 (107/4480, Estonian)
G=0.016 (62/3854, ALSPAC)
G=0.015 (56/3708, TWINSUK)
G=0.02 (11/600, NorthernSweden)
G=0.11 (24/216, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SCGB1B2P : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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.p12 chr 19 NC_000019.10:g.34588527C>G
GRCh37.p13 chr 19 NC_000019.9:g.35079432C>G
Gene: SCGB1B2P, secretoglobin family 1B member 2, pseudogene (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SCGB1B2P transcript NR_027620.3:n. N/A Intron 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

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 125568 C=0.98125 G=0.01875
gnomAD - Genomes Global Study-wide 31396 C=0.9817 G=0.0183
gnomAD - Genomes European Sub 18906 C=0.9811 G=0.0189
gnomAD - Genomes African Sub 8710 C=0.995 G=0.005
gnomAD - Genomes East Asian Sub 1556 C=0.904 G=0.096
gnomAD - Genomes Other Sub 1088 C=0.988 G=0.012
gnomAD - Genomes American Sub 846 C=0.99 G=0.01
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=1.00 G=0.00
1000Genomes Global Study-wide 5008 C=0.970 G=0.030
1000Genomes African Sub 1322 C=0.997 G=0.003
1000Genomes East Asian Sub 1008 C=0.902 G=0.098
1000Genomes Europe Sub 1006 C=0.983 G=0.017
1000Genomes South Asian Sub 978 C=0.98 G=0.02
1000Genomes American Sub 694 C=0.98 G=0.02
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.976 G=0.024
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.984 G=0.016
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.985 G=0.015
Northern Sweden ACPOP Study-wide 600 C=0.98 G=0.02
A Vietnamese Genetic Variation Database Global Study-wide 216 C=0.89 G=0.11
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 C= G Note
GRCh38.p12 chr 19 NC_000019.10:g.34588527= NC_000019.10:g.34588527C>G
GRCh37.p13 chr 19 NC_000019.9:g.35079432= NC_000019.9:g.35079432C>G
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#.

25 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 WIAF ss2343 Sep 19, 2000 (36)
2 1000GENOMES ss237665337 Jul 15, 2010 (132)
3 1000GENOMES ss243873246 Jul 15, 2010 (132)
4 GMI ss283195364 May 04, 2012 (137)
5 SSMP ss661822066 Apr 25, 2013 (138)
6 EVA-GONL ss994262416 Aug 21, 2014 (142)
7 JMKIDD_LAB ss1081878905 Aug 21, 2014 (142)
8 1000GENOMES ss1363021258 Aug 21, 2014 (142)
9 EVA_UK10K_ALSPAC ss1637897507 Apr 01, 2015 (144)
10 EVA_UK10K_TWINSUK ss1680891540 Apr 01, 2015 (144)
11 EVA_DECODE ss1698315825 Apr 01, 2015 (144)
12 WEILL_CORNELL_DGM ss1937756173 Feb 12, 2016 (147)
13 USC_VALOUEV ss2158193993 Dec 20, 2016 (150)
14 HUMAN_LONGEVITY ss2225481628 Dec 20, 2016 (150)
15 TOPMED ss2391169156 Dec 20, 2016 (150)
16 GRF ss2702802108 Nov 08, 2017 (151)
17 GNOMAD ss2962435438 Nov 08, 2017 (151)
18 SWEGEN ss3017407032 Nov 08, 2017 (151)
19 TOPMED ss3292318531 Nov 08, 2017 (151)
20 CSHL ss3352285953 Nov 08, 2017 (151)
21 EGCUT_WGS ss3684183288 Jul 13, 2019 (153)
22 EVA_DECODE ss3702693723 Jul 13, 2019 (153)
23 ACPOP ss3743006140 Jul 13, 2019 (153)
24 EVA ss3756020258 Jul 13, 2019 (153)
25 KHV_HUMAN_GENOMES ss3821268312 Jul 13, 2019 (153)
26 1000Genomes NC_000019.9 - 35079432 Oct 12, 2018 (152)
27 The Avon Longitudinal Study of Parents and Children NC_000019.9 - 35079432 Oct 12, 2018 (152)
28 Genetic variation in the Estonian population NC_000019.9 - 35079432 Oct 12, 2018 (152)
29 gnomAD - Genomes NC_000019.9 - 35079432 Jul 13, 2019 (153)
30 Northern Sweden NC_000019.9 - 35079432 Jul 13, 2019 (153)
31 TopMed NC_000019.10 - 34588527 Oct 12, 2018 (152)
32 UK 10K study - Twins NC_000019.9 - 35079432 Oct 12, 2018 (152)
33 A Vietnamese Genetic Variation Database NC_000019.9 - 35079432 Jul 13, 2019 (153)
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
ss283195364, ss1698315825 NC_000019.8:39771271:C:G NC_000019.10:34588526:C:G (self)
76423063, 42330834, 29921536, 208606592, 16291005, 42330834, 9351067, ss237665337, ss243873246, ss661822066, ss994262416, ss1081878905, ss1363021258, ss1637897507, ss1680891540, ss1937756173, ss2158193993, ss2391169156, ss2702802108, ss2962435438, ss3017407032, ss3352285953, ss3684183288, ss3743006140, ss3756020258 NC_000019.9:35079431:C:G NC_000019.10:34588526:C:G (self)
180378701, ss2225481628, ss3292318531, ss3702693723, ss3821268312 NC_000019.10:34588526:C:G NC_000019.10:34588526:C:G (self)
ss2343 NT_011109.16:7347649:C:G NC_000019.10:34588526:C:G (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 rs2316

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.post308+0fe9b3b