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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs142804984

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:51890692 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000393 (104/264690, TOPMED)
C=0.000056 (14/250362, GnomAD_exome)
C=0.000024 (4/163766, ALFA) (+ 4 more)
C=0.000278 (39/140294, GnomAD)
C=0.000041 (5/121354, ExAC)
C=0.00058 (46/78696, PAGE_STUDY)
C=0.00031 (4/13006, GO-ESP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ZNF649 : Missense Variant
ZNF649-AS1 : 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 180170 T=0.999956 C=0.000044
European Sub 156990 T=1.000000 C=0.000000
African Sub 9128 T=0.9993 C=0.0007
African Others Sub 352 T=0.997 C=0.003
African American Sub 8776 T=0.9994 C=0.0006
Asian Sub 3336 T=1.0000 C=0.0000
East Asian Sub 2684 T=1.0000 C=0.0000
Other Asian Sub 652 T=1.000 C=0.000
Latin American 1 Sub 442 T=1.000 C=0.000
Latin American 2 Sub 950 T=0.999 C=0.001
South Asian Sub 280 T=1.000 C=0.000
Other Sub 9044 T=0.9999 C=0.0001


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 T=0.999607 C=0.000393
gnomAD - Exomes Global Study-wide 250362 T=0.999944 C=0.000056
gnomAD - Exomes European Sub 134296 T=1.000000 C=0.000000
gnomAD - Exomes Asian Sub 49010 T=1.00000 C=0.00000
gnomAD - Exomes American Sub 34592 T=0.99988 C=0.00012
gnomAD - Exomes African Sub 16256 T=0.99938 C=0.00062
gnomAD - Exomes Ashkenazi Jewish Sub 10074 T=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6134 T=1.0000 C=0.0000
Allele Frequency Aggregator Total Global 163766 T=0.999976 C=0.000024
Allele Frequency Aggregator European Sub 146858 T=1.000000 C=0.000000
Allele Frequency Aggregator Other Sub 7610 T=0.9999 C=0.0001
Allele Frequency Aggregator African Sub 4290 T=0.9995 C=0.0005
Allele Frequency Aggregator Asian Sub 3336 T=1.0000 C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 950 T=0.999 C=0.001
Allele Frequency Aggregator Latin American 1 Sub 442 T=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 280 T=1.000 C=0.000
gnomAD - Genomes Global Study-wide 140294 T=0.999722 C=0.000278
gnomAD - Genomes European Sub 75952 T=1.00000 C=0.00000
gnomAD - Genomes African Sub 42068 T=0.99912 C=0.00088
gnomAD - Genomes American Sub 13664 T=0.99993 C=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3134 T=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2152 T=0.9995 C=0.0005
ExAC Global Study-wide 121354 T=0.999959 C=0.000041
ExAC Europe Sub 73306 T=1.00000 C=0.00000
ExAC Asian Sub 25156 T=1.00000 C=0.00000
ExAC American Sub 11578 T=1.00000 C=0.00000
ExAC African Sub 10406 T=0.99952 C=0.00048
ExAC Other Sub 908 T=1.000 C=0.000
The PAGE Study Global Study-wide 78696 T=0.99942 C=0.00058
The PAGE Study AfricanAmerican Sub 32514 T=0.99892 C=0.00108
The PAGE Study Mexican Sub 10810 T=0.99991 C=0.00009
The PAGE Study Asian Sub 8316 T=1.0000 C=0.0000
The PAGE Study PuertoRican Sub 7918 T=1.0000 C=0.0000
The PAGE Study NativeHawaiian Sub 4532 T=1.0000 C=0.0000
The PAGE Study Cuban Sub 4230 T=0.9998 C=0.0002
The PAGE Study Dominican Sub 3828 T=0.9982 C=0.0018
The PAGE Study CentralAmerican Sub 2450 T=0.9996 C=0.0004
The PAGE Study SouthAmerican Sub 1982 T=1.0000 C=0.0000
The PAGE Study NativeAmerican Sub 1260 T=0.9992 C=0.0008
The PAGE Study SouthAsian Sub 856 T=1.000 C=0.000
GO Exome Sequencing Project Global Study-wide 13006 T=0.99969 C=0.00031
GO Exome Sequencing Project European American Sub 8600 T=1.0000 C=0.0000
GO Exome Sequencing Project African American Sub 4406 T=0.9991 C=0.0009
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.51890692T>C
GRCh37.p13 chr 19 NC_000019.9:g.52393945T>C
Gene: ZNF649, zinc finger protein 649 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ZNF649 transcript NM_023074.4:c.1444A>G K [AAA] > E [GAA] Coding Sequence Variant
zinc finger protein 649 NP_075562.2:p.Lys482Glu K (Lys) > E (Glu) Missense Variant
ZNF649 transcript variant X1 XM_047439238.1:c.1432A>G K [AAA] > E [GAA] Coding Sequence Variant
zinc finger protein 649 isoform X1 XP_047295194.1:p.Lys478Glu K (Lys) > E (Glu) Missense Variant
ZNF649 transcript variant X2 XM_047439239.1:c.1009A>G K [AAA] > E [GAA] Coding Sequence Variant
zinc finger protein 649 isoform X2 XP_047295195.1:p.Lys337Glu K (Lys) > E (Glu) Missense Variant
Gene: ZNF649-AS1, ZNF649 antisense RNA 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ZNF649-AS1 transcript NR_110733.1: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

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 T= C
GRCh38.p14 chr 19 NC_000019.10:g.51890692= NC_000019.10:g.51890692T>C
GRCh37.p13 chr 19 NC_000019.9:g.52393945= NC_000019.9:g.52393945T>C
ZNF649 transcript NM_023074.4:c.1444= NM_023074.4:c.1444A>G
ZNF649 transcript NM_023074.3:c.1444= NM_023074.3:c.1444A>G
ZNF649 transcript variant X1 XM_047439238.1:c.1432= XM_047439238.1:c.1432A>G
ZNF649 transcript variant X2 XM_047439239.1:c.1009= XM_047439239.1:c.1009A>G
zinc finger protein 649 NP_075562.2:p.Lys482= NP_075562.2:p.Lys482Glu
zinc finger protein 649 isoform X1 XP_047295194.1:p.Lys478= XP_047295194.1:p.Lys478Glu
zinc finger protein 649 isoform X2 XP_047295195.1:p.Lys337= XP_047295195.1:p.Lys337Glu
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#.

31 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342507771 May 09, 2011 (134)
2 EXOME_CHIP ss491552713 May 04, 2012 (137)
3 ILLUMINA ss780749302 Sep 08, 2015 (146)
4 ILLUMINA ss783427272 Sep 08, 2015 (146)
5 EVA_EXAC ss1693769067 Apr 01, 2015 (144)
6 ILLUMINA ss1752293009 Sep 08, 2015 (146)
7 ILLUMINA ss1917941251 Feb 12, 2016 (147)
8 ILLUMINA ss1946540849 Feb 12, 2016 (147)
9 ILLUMINA ss1959878884 Feb 12, 2016 (147)
10 HUMAN_LONGEVITY ss2226440102 Dec 20, 2016 (150)
11 GNOMAD ss2744256471 Nov 08, 2017 (151)
12 GNOMAD ss2750271629 Nov 08, 2017 (151)
13 GNOMAD ss2963963120 Nov 08, 2017 (151)
14 AFFY ss2985151002 Nov 08, 2017 (151)
15 ILLUMINA ss3021920674 Nov 08, 2017 (151)
16 ILLUMINA ss3627956360 Oct 12, 2018 (152)
17 ILLUMINA ss3634742627 Oct 12, 2018 (152)
18 ILLUMINA ss3640449933 Oct 12, 2018 (152)
19 ILLUMINA ss3644729391 Oct 12, 2018 (152)
20 ILLUMINA ss3652347592 Oct 12, 2018 (152)
21 ILLUMINA ss3653921961 Oct 12, 2018 (152)
22 ILLUMINA ss3725741039 Jul 13, 2019 (153)
23 ILLUMINA ss3744468555 Jul 13, 2019 (153)
24 ILLUMINA ss3745042623 Jul 13, 2019 (153)
25 PAGE_CC ss3772023273 Jul 13, 2019 (153)
26 ILLUMINA ss3772539624 Jul 13, 2019 (153)
27 EVA ss3825322623 Apr 27, 2020 (154)
28 TOPMED ss5077944994 Apr 27, 2021 (155)
29 HUGCELL_USP ss5500066162 Oct 13, 2022 (156)
30 EVA ss5847849860 Oct 13, 2022 (156)
31 EVA ss5953992648 Oct 13, 2022 (156)
32 ExAC NC_000019.9 - 52393945 Oct 12, 2018 (152)
33 gnomAD - Genomes NC_000019.10 - 51890692 Apr 27, 2021 (155)
34 gnomAD - Exomes NC_000019.9 - 52393945 Jul 13, 2019 (153)
35 GO Exome Sequencing Project NC_000019.9 - 52393945 Oct 12, 2018 (152)
36 The PAGE Study NC_000019.10 - 51890692 Jul 13, 2019 (153)
37 TopMed NC_000019.10 - 51890692 Apr 27, 2021 (155)
38 ALFA NC_000019.10 - 51890692 Apr 27, 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
4285651, 13570107, 1779560, ss342507771, ss491552713, ss780749302, ss783427272, ss1693769067, ss1752293009, ss1917941251, ss1946540849, ss1959878884, ss2744256471, ss2750271629, ss2963963120, ss2985151002, ss3021920674, ss3627956360, ss3634742627, ss3640449933, ss3644729391, ss3652347592, ss3653921961, ss3744468555, ss3745042623, ss3772539624, ss3825322623, ss5847849860, ss5953992648 NC_000019.9:52393944:T:C NC_000019.10:51890691:T:C (self)
542771332, 1244742, 293490658, 9172261023, ss2226440102, ss3725741039, ss3772023273, ss5077944994, ss5500066162 NC_000019.10:51890691:T:C NC_000019.10:51890691:T:C (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 rs142804984

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