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dbSNP Short Genetic Variations

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.

rs61749179

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr11:66850388 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00096 (236/246196, GnomAD)
A=0.00090 (113/125568, TOPMED)
A=0.00087 (106/121180, ExAC) (+ 6 more)
A=0.0006 (20/30936, GnomAD)
A=0.0013 (17/12990, GO-ESP)
A=0.000 (2/5008, 1000G)
A=0.000 (2/4480, Estonian)
A=0.003 (12/3854, ALSPAC)
A=0.001 (5/3708, TWINSUK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PC : Synonymous 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 11 NC_000011.10:g.66850388G>A
GRCh37.p13 chr 11 NC_000011.9:g.66617859G>A
PC RefSeqGene NG_008319.1:g.112989C>T
Gene: PC, pyruvate carboxylase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PC transcript variant 2 NM_022172.2:c.2550C>T C [TGC] > C [TGT] Coding Sequence Variant
pyruvate carboxylase, mitochondrial precursor NP_071504.2:p.Cys850= C (Cys) > C (Cys) Synonymous Variant
PC transcript variant 1 NM_000920.3:c.2550C>T C [TGC] > C [TGT] Coding Sequence Variant
pyruvate carboxylase, mitochondrial precursor NP_000911.2:p.Cys850= C (Cys) > C (Cys) Synonymous Variant
PC transcript variant 3 NM_001040716.1:c.2550C>T C [TGC] > C [TGT] Coding Sequence Variant
pyruvate carboxylase, mitochondrial precursor NP_001035806.1:p.Cys850= C (Cys) > C (Cys) Synonymous Variant
PC transcript variant X1 XM_017017868.1:c.2550C>T C [TGC] > C [TGT] Coding Sequence Variant
pyruvate carboxylase, mitochondrial isoform X1 XP_016873357.1:p.Cys850= C (Cys) > C (Cys) Synonymous Variant
PC transcript variant X2 XM_017017869.1:c.2550C>T C [TGC] > C [TGT] Coding Sequence Variant
pyruvate carboxylase, mitochondrial isoform X1 XP_016873358.1:p.Cys850= C (Cys) > C (Cys) Synonymous Variant
PC transcript variant X3 XM_017017870.1:c.2550C>T C [TGC] > C [TGT] Coding Sequence Variant
pyruvate carboxylase, mitochondrial isoform X1 XP_016873359.1:p.Cys850= C (Cys) > C (Cys) Synonymous Variant
PC transcript variant X4 XM_017017871.1:c.2550C>T C [TGC] > C [TGT] Coding Sequence Variant
pyruvate carboxylase, mitochondrial isoform X1 XP_016873360.1:p.Cys850= C (Cys) > C (Cys) Synonymous Variant
PC transcript variant X5 XM_006718578.3:c.2550C>T C [TGC] > C [TGT] Coding Sequence Variant
pyruvate carboxylase, mitochondrial isoform X1 XP_006718641.1:p.Cys850= C (Cys) > C (Cys) Synonymous Variant
PC transcript variant X7 XM_005274031.4:c.2550C>T C [TGC] > C [TGT] Coding Sequence Variant
pyruvate carboxylase, mitochondrial isoform X1 XP_005274088.1:p.Cys850= C (Cys) > C (Cys) Synonymous Variant
PC transcript variant X9 XM_011545086.2:c.2550C>T C [TGC] > C [TGT] Coding Sequence Variant
pyruvate carboxylase, mitochondrial isoform X1 XP_011543388.1:p.Cys850= C (Cys) > C (Cys) Synonymous Variant
PC transcript variant X8 XM_005274032.4:c.2550C>T C [TGC] > C [TGT] Coding Sequence Variant
pyruvate carboxylase, mitochondrial isoform X1 XP_005274089.1:p.Cys850= C (Cys) > C (Cys) Synonymous Variant
PC transcript variant X10 XM_011545087.2:c.1254C>T C [TGC] > C [TGT] Coding Sequence Variant
pyruvate carboxylase, mitochondrial isoform X2 XP_011543389.1:p.Cys418= C (Cys) > C (Cys) Synonymous Variant
PC transcript variant X11 XM_006718579.3:c.1029C>T C [TGC] > C [TGT] Coding Sequence Variant
pyruvate carboxylase, mitochondrial isoform X3 XP_006718642.1:p.Cys343= C (Cys) > C (Cys) Synonymous Variant
PC transcript variant X6 XM_017017872.2:c.2550C>T C [TGC] > C [TGT] Coding Sequence Variant
pyruvate carboxylase, mitochondrial isoform X1 XP_016873361.1:p.Cys850= C (Cys) > C (Cys) 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.

Allele: A (allele ID: 142283 )
ClinVar Accession Disease Names Clinical Significance
RCV000127316.3 not specified Benign
RCV000347109.1 Pyruvate carboxylase deficiency Uncertain-Significance
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
gnomAD - Exomes Global Study-wide 246196 G=0.99904 A=0.00096
gnomAD - Exomes European Sub 133952 G=0.99874 A=0.00126
gnomAD - Exomes Asian Sub 48028 G=0.9992 A=0.0008
gnomAD - Exomes American Sub 33582 G=0.9993 A=0.0007
gnomAD - Exomes African Sub 15300 G=0.9999 A=0.0001
gnomAD - Exomes Ashkenazi Jewish Sub 9848 G=1.000 A=0.000
gnomAD - Exomes Other Sub 5486 G=1.000 A=0.000
TopMed Global Study-wide 125568 G=0.99910 A=0.00090
ExAC Global Study-wide 121180 G=0.99913 A=0.00087
ExAC Europe Sub 73174 G=0.9989 A=0.0011
ExAC Asian Sub 25154 G=0.9992 A=0.0008
ExAC American Sub 11568 G=0.9995 A=0.0005
ExAC African Sub 10378 G=0.9999 A=0.0001
ExAC Other Sub 906 G=1.00 A=0.00
gnomAD - Genomes Global Study-wide 30936 G=0.9994 A=0.0006
gnomAD - Genomes European Sub 18476 G=0.9991 A=0.0009
gnomAD - Genomes African Sub 8716 G=1.000 A=0.000
gnomAD - Genomes East Asian Sub 1622 G=1.000 A=0.000
gnomAD - Genomes Other Sub 982 G=1.00 A=0.00
gnomAD - Genomes American Sub 838 G=1.00 A=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 302 G=1.00 A=0.00
GO Exome Sequencing Project Global Study-wide 12990 G=0.9987 A=0.0013
GO Exome Sequencing Project European American Sub 8590 G=0.998 A=0.002
GO Exome Sequencing Project African American Sub 4400 G=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=1.000 A=0.000
1000Genomes African Sub 1322 G=1.000 A=0.000
1000Genomes East Asian Sub 1008 G=1.000 A=0.000
1000Genomes Europe Sub 1006 G=0.999 A=0.001
1000Genomes South Asian Sub 978 G=1.00 A=0.00
1000Genomes American Sub 694 G=1.00 A=0.00
Genetic variation in the Estonian population Estonian Study-wide 4480 G=1.000 A=0.000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.997 A=0.003
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.999 A=0.001
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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 Note
GRCh38.p12 chr 11 NC_000011.10:g.66850388G= NC_000011.10:g.66850388G>A
GRCh37.p13 chr 11 NC_000011.9:g.66617859G= NC_000011.9:g.66617859G>A
PC RefSeqGene NG_008319.1:g.112989C= NG_008319.1:g.112989C>T
PC transcript variant 1 NM_000920.3:c.2550C= NM_000920.3:c.2550C>T
PC transcript variant 2 NM_022172.2:c.2550C= NM_022172.2:c.2550C>T
PC transcript variant 3 NM_001040716.1:c.2550C= NM_001040716.1:c.2550C>T
PC transcript variant X7 XM_005274031.4:c.2550C= XM_005274031.4:c.2550C>T
PC transcript variant X2 XM_005274031.1:c.2550C= XM_005274031.1:c.2550C>T
PC transcript variant X8 XM_005274032.4:c.2550C= XM_005274032.4:c.2550C>T
PC transcript variant X3 XM_005274032.1:c.2550C= XM_005274032.1:c.2550C>T
PC transcript variant X5 XM_006718578.3:c.2550C= XM_006718578.3:c.2550C>T
PC transcript variant X11 XM_006718579.3:c.1029C= XM_006718579.3:c.1029C>T
PC transcript variant X6 XM_017017872.2:c.2550C= XM_017017872.2:c.2550C>T
PC transcript variant X9 XM_011545086.2:c.2550C= XM_011545086.2:c.2550C>T
PC transcript variant X10 XM_011545087.2:c.1254C= XM_011545087.2:c.1254C>T
PC transcript variant X1 XM_017017868.1:c.2550C= XM_017017868.1:c.2550C>T
PC transcript variant X2 XM_017017869.1:c.2550C= XM_017017869.1:c.2550C>T
PC transcript variant X3 XM_017017870.1:c.2550C= XM_017017870.1:c.2550C>T
PC transcript variant X4 XM_017017871.1:c.2550C= XM_017017871.1:c.2550C>T
pyruvate carboxylase, mitochondrial precursor NP_000911.2:p.Cys850= NP_000911.2:p.Cys850=
pyruvate carboxylase, mitochondrial precursor NP_071504.2:p.Cys850= NP_071504.2:p.Cys850=
pyruvate carboxylase, mitochondrial precursor NP_001035806.1:p.Cys850= NP_001035806.1:p.Cys850=
pyruvate carboxylase, mitochondrial isoform X1 XP_005274088.1:p.Cys850= XP_005274088.1:p.Cys850=
pyruvate carboxylase, mitochondrial isoform X1 XP_005274089.1:p.Cys850= XP_005274089.1:p.Cys850=
pyruvate carboxylase, mitochondrial isoform X1 XP_006718641.1:p.Cys850= XP_006718641.1:p.Cys850=
pyruvate carboxylase, mitochondrial isoform X3 XP_006718642.1:p.Cys343= XP_006718642.1:p.Cys343=
pyruvate carboxylase, mitochondrial isoform X1 XP_016873361.1:p.Cys850= XP_016873361.1:p.Cys850=
pyruvate carboxylase, mitochondrial isoform X1 XP_011543388.1:p.Cys850= XP_011543388.1:p.Cys850=
pyruvate carboxylase, mitochondrial isoform X2 XP_011543389.1:p.Cys418= XP_011543389.1:p.Cys418=
pyruvate carboxylase, mitochondrial isoform X1 XP_016873357.1:p.Cys850= XP_016873357.1:p.Cys850=
pyruvate carboxylase, mitochondrial isoform X1 XP_016873358.1:p.Cys850= XP_016873358.1:p.Cys850=
pyruvate carboxylase, mitochondrial isoform X1 XP_016873359.1:p.Cys850= XP_016873359.1:p.Cys850=
pyruvate carboxylase, mitochondrial isoform X1 XP_016873360.1:p.Cys850= XP_016873360.1:p.Cys850=
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#.

17 SubSNP, 9 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CANCER-GENOME ss86346163 Mar 23, 2008 (129)
2 NHLBI-ESP ss342333215 May 09, 2011 (134)
3 1000GENOMES ss488968025 May 04, 2012 (137)
4 1000GENOMES ss1341665094 Aug 21, 2014 (142)
5 CLINVAR ss1457618724 Nov 23, 2014 (142)
6 EVA_DECODE ss1598282749 Apr 01, 2015 (144)
7 EVA_UK10K_ALSPAC ss1626790664 Apr 01, 2015 (144)
8 EVA_UK10K_TWINSUK ss1669784697 Apr 01, 2015 (144)
9 EVA_EXAC ss1690495697 Apr 01, 2015 (144)
10 HUMAN_LONGEVITY ss2183141037 Dec 20, 2016 (150)
11 TOPMED ss2346578428 Dec 20, 2016 (150)
12 GNOMAD ss2739168592 Nov 08, 2017 (151)
13 GNOMAD ss2748672090 Nov 08, 2017 (151)
14 GNOMAD ss2900786476 Nov 08, 2017 (151)
15 SWEGEN ss3008254680 Nov 08, 2017 (151)
16 TOPMED ss3147959129 Nov 08, 2017 (151)
17 ILLUMINA ss3625603080 Oct 12, 2018 (152)
18 1000Genomes NC_000011.9 - 66617859 Oct 12, 2018 (152)
19 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 66617859 Oct 12, 2018 (152)
20 Genetic variation in the Estonian population NC_000011.9 - 66617859 Oct 12, 2018 (152)
21 ExAC NC_000011.9 - 66617859 Oct 12, 2018 (152)
22 gnomAD - Genomes NC_000011.9 - 66617859 Oct 12, 2018 (152)
23 gnomAD - Exomes NC_000011.9 - 66617859 Oct 12, 2018 (152)
24 GO Exome Sequencing Project NC_000011.9 - 66617859 Oct 12, 2018 (152)
25 TopMed NC_000011.10 - 66850388 Oct 12, 2018 (152)
26 UK 10K study - Twins NC_000011.9 - 66617859 Oct 12, 2018 (152)
27 ClinVar RCV000127316.3 Oct 12, 2018 (152)
28 ClinVar RCV000347109.1 Oct 12, 2018 (152)
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
ss1598282749 NC_000011.8:66374434:G= NC_000011.10:66850387:G= (self)
54201169, 30095078, 21328997, 760860, 34487998, 6632663, 1100551, 30095078, ss342333215, ss488968025, ss1341665094, ss1626790664, ss1669784697, ss1690495697, ss2346578428, ss2739168592, ss2748672090, ss2900786476, ss3008254680, ss3625603080 NC_000011.9:66617858:G= NC_000011.10:66850387:G= (self)
65428632, ss1457618724, ss2183141037, ss3147959129 NC_000011.10:66850387:G= NC_000011.10:66850387:G= (self)
ss86346163 NT_167190.1:11923653:G= NC_000011.10:66850387:G= (self)
ss1598282749 NC_000011.8:66374434:G>A NC_000011.10:66850387:G>A (self)
54201169, 30095078, 21328997, 760860, 34487998, 6632663, 1100551, 30095078, ss342333215, ss488968025, ss1341665094, ss1626790664, ss1669784697, ss1690495697, ss2346578428, ss2739168592, ss2748672090, ss2900786476, ss3008254680, ss3625603080 NC_000011.9:66617858:G>A NC_000011.10:66850387:G>A (self)
RCV000127316.3, RCV000347109.1, 65428632, ss1457618724, ss2183141037, ss3147959129 NC_000011.10:66850387:G>A NC_000011.10:66850387:G>A (self)
ss86346163 NT_167190.1:11923653:G>A NC_000011.10:66850387: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 rs61749179

Genomic regions, transcripts, and products
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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.post76+b4aec9c