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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.

rs149749354

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:161785902 (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 / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000036 (9/251092, GnomAD_exome)
A=0.000042 (5/118938, ExAC)
A=0.00000 (0/14048, ALFA) (+ 4 more)
T=0.00000 (0/14048, ALFA)
A=0.00015 (2/13006, GO-ESP)
A=0.0000 (0/3854, ALSPAC)
A=0.0003 (1/3708, TWINSUK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PRKN : Synonymous 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 14048 G=1.00000 A=0.00000, T=0.00000
European Sub 9690 G=1.0000 A=0.0000, T=0.0000
African Sub 2898 G=1.0000 A=0.0000, T=0.0000
African Others Sub 114 G=1.000 A=0.000, T=0.000
African American Sub 2784 G=1.0000 A=0.0000, T=0.0000
Asian Sub 112 G=1.000 A=0.000, T=0.000
East Asian Sub 86 G=1.00 A=0.00, T=0.00
Other Asian Sub 26 G=1.00 A=0.00, T=0.00
Latin American 1 Sub 146 G=1.000 A=0.000, T=0.000
Latin American 2 Sub 608 G=1.000 A=0.000, T=0.000
South Asian Sub 98 G=1.00 A=0.00, T=0.00
Other Sub 496 G=1.000 A=0.000, T=0.000


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
gnomAD - Exomes Global Study-wide 251092 G=0.999964 A=0.000036
gnomAD - Exomes European Sub 135144 G=0.999993 A=0.000007
gnomAD - Exomes Asian Sub 48942 G=0.99994 A=0.00006
gnomAD - Exomes American Sub 34558 G=0.99988 A=0.00012
gnomAD - Exomes African Sub 16236 G=0.99994 A=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10076 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6136 G=1.0000 A=0.0000
ExAC Global Study-wide 118938 G=0.999958 A=0.000042
ExAC Europe Sub 71830 G=0.99999 A=0.00001
ExAC Asian Sub 24702 G=0.99992 A=0.00008
ExAC American Sub 11324 G=0.99991 A=0.00009
ExAC African Sub 10198 G=0.99990 A=0.00010
ExAC Other Sub 884 G=1.000 A=0.000
Allele Frequency Aggregator Total Global 14048 G=1.00000 A=0.00000, T=0.00000
Allele Frequency Aggregator European Sub 9690 G=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator African Sub 2898 G=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 608 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Other Sub 496 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00, T=0.00
GO Exome Sequencing Project Global Study-wide 13006 G=0.99985 A=0.00015
GO Exome Sequencing Project European American Sub 8600 G=1.0000 A=0.0000
GO Exome Sequencing Project African American Sub 4406 G=0.9995 A=0.0005
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=1.0000 A=0.0000
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9997 A=0.0003
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 6 NC_000006.12:g.161785902G>A
GRCh38.p14 chr 6 NC_000006.12:g.161785902G>C
GRCh38.p14 chr 6 NC_000006.12:g.161785902G>T
GRCh37.p13 chr 6 NC_000006.11:g.162206934G>A
GRCh37.p13 chr 6 NC_000006.11:g.162206934G>C
GRCh37.p13 chr 6 NC_000006.11:g.162206934G>T
PRKN RefSeqGene NG_008289.2:g.946901C>T
PRKN RefSeqGene NG_008289.2:g.946901C>G
PRKN RefSeqGene NG_008289.2:g.946901C>A
Gene: PRKN, parkin RBR E3 ubiquitin protein ligase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PRKN transcript variant 1 NM_004562.3:c.741C>T P [CCC] > P [CCT] Coding Sequence Variant
E3 ubiquitin-protein ligase parkin isoform 1 NP_004553.2:p.Pro247= P (Pro) > P (Pro) Synonymous Variant
PRKN transcript variant 1 NM_004562.3:c.741C>G P [CCC] > P [CCG] Coding Sequence Variant
E3 ubiquitin-protein ligase parkin isoform 1 NP_004553.2:p.Pro247= P (Pro) > P (Pro) Synonymous Variant
PRKN transcript variant 1 NM_004562.3:c.741C>A P [CCC] > P [CCA] Coding Sequence Variant
E3 ubiquitin-protein ligase parkin isoform 1 NP_004553.2:p.Pro247= P (Pro) > P (Pro) Synonymous Variant
PRKN transcript variant 2 NM_013987.3:c.657C>T P [CCC] > P [CCT] Coding Sequence Variant
E3 ubiquitin-protein ligase parkin isoform 2 NP_054642.2:p.Pro219= P (Pro) > P (Pro) Synonymous Variant
PRKN transcript variant 2 NM_013987.3:c.657C>G P [CCC] > P [CCG] Coding Sequence Variant
E3 ubiquitin-protein ligase parkin isoform 2 NP_054642.2:p.Pro219= P (Pro) > P (Pro) Synonymous Variant
PRKN transcript variant 2 NM_013987.3:c.657C>A P [CCC] > P [CCA] Coding Sequence Variant
E3 ubiquitin-protein ligase parkin isoform 2 NP_054642.2:p.Pro219= P (Pro) > P (Pro) Synonymous Variant
PRKN transcript variant 3 NM_013988.3:c.294C>T P [CCC] > P [CCT] Coding Sequence Variant
E3 ubiquitin-protein ligase parkin isoform 3 NP_054643.2:p.Pro98= P (Pro) > P (Pro) Synonymous Variant
PRKN transcript variant 3 NM_013988.3:c.294C>G P [CCC] > P [CCG] Coding Sequence Variant
E3 ubiquitin-protein ligase parkin isoform 3 NP_054643.2:p.Pro98= P (Pro) > P (Pro) Synonymous Variant
PRKN transcript variant 3 NM_013988.3:c.294C>A P [CCC] > P [CCA] Coding Sequence Variant
E3 ubiquitin-protein ligase parkin isoform 3 NP_054643.2:p.Pro98= P (Pro) > P (Pro) Synonymous Variant
PRKN transcript variant X1 XM_017010908.2:c.855C>T P [CCC] > P [CCT] Coding Sequence Variant
E3 ubiquitin-protein ligase parkin isoform X1 XP_016866397.1:p.Pro285= P (Pro) > P (Pro) Synonymous Variant
PRKN transcript variant X1 XM_017010908.2:c.855C>G P [CCC] > P [CCG] Coding Sequence Variant
E3 ubiquitin-protein ligase parkin isoform X1 XP_016866397.1:p.Pro285= P (Pro) > P (Pro) Synonymous Variant
PRKN transcript variant X1 XM_017010908.2:c.855C>A P [CCC] > P [CCA] Coding Sequence Variant
E3 ubiquitin-protein ligase parkin isoform X1 XP_016866397.1:p.Pro285= P (Pro) > P (Pro) Synonymous Variant
PRKN transcript variant X2 XM_011535863.2:c.738C>T P [CCC] > P [CCT] Coding Sequence Variant
E3 ubiquitin-protein ligase parkin isoform X2 XP_011534165.1:p.Pro246= P (Pro) > P (Pro) Synonymous Variant
PRKN transcript variant X2 XM_011535863.2:c.738C>G P [CCC] > P [CCG] Coding Sequence Variant
E3 ubiquitin-protein ligase parkin isoform X2 XP_011534165.1:p.Pro246= P (Pro) > P (Pro) Synonymous Variant
PRKN transcript variant X2 XM_011535863.2:c.738C>A P [CCC] > P [CCA] Coding Sequence Variant
E3 ubiquitin-protein ligase parkin isoform X2 XP_011534165.1:p.Pro246= P (Pro) > P (Pro) Synonymous Variant
PRKN transcript variant X3 XM_024446449.2:c.504C>T P [CCC] > P [CCT] Coding Sequence Variant
E3 ubiquitin-protein ligase parkin isoform X3 XP_024302217.1:p.Pro168= P (Pro) > P (Pro) Synonymous Variant
PRKN transcript variant X3 XM_024446449.2:c.504C>G P [CCC] > P [CCG] Coding Sequence Variant
E3 ubiquitin-protein ligase parkin isoform X3 XP_024302217.1:p.Pro168= P (Pro) > P (Pro) Synonymous Variant
PRKN transcript variant X3 XM_024446449.2:c.504C>A P [CCC] > P [CCA] Coding Sequence Variant
E3 ubiquitin-protein ligase parkin isoform X3 XP_024302217.1:p.Pro168= P (Pro) > P (Pro) 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: 1642394 )
ClinVar Accession Disease Names Clinical Significance
RCV002103650.3 not provided Likely-Benign
Allele: T (allele ID: 1599553 )
ClinVar Accession Disease Names Clinical Significance
RCV002094734.3 not provided Likely-Benign
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 C T
GRCh38.p14 chr 6 NC_000006.12:g.161785902= NC_000006.12:g.161785902G>A NC_000006.12:g.161785902G>C NC_000006.12:g.161785902G>T
GRCh37.p13 chr 6 NC_000006.11:g.162206934= NC_000006.11:g.162206934G>A NC_000006.11:g.162206934G>C NC_000006.11:g.162206934G>T
PRKN RefSeqGene NG_008289.2:g.946901= NG_008289.2:g.946901C>T NG_008289.2:g.946901C>G NG_008289.2:g.946901C>A
PRKN transcript variant 1 NM_004562.3:c.741= NM_004562.3:c.741C>T NM_004562.3:c.741C>G NM_004562.3:c.741C>A
PRKN transcript variant 1 NM_004562.2:c.741= NM_004562.2:c.741C>T NM_004562.2:c.741C>G NM_004562.2:c.741C>A
PRKN transcript variant 2 NM_013987.3:c.657= NM_013987.3:c.657C>T NM_013987.3:c.657C>G NM_013987.3:c.657C>A
PRKN transcript variant 2 NM_013987.2:c.657= NM_013987.2:c.657C>T NM_013987.2:c.657C>G NM_013987.2:c.657C>A
PRKN transcript variant 3 NM_013988.3:c.294= NM_013988.3:c.294C>T NM_013988.3:c.294C>G NM_013988.3:c.294C>A
PRKN transcript variant 3 NM_013988.2:c.294= NM_013988.2:c.294C>T NM_013988.2:c.294C>G NM_013988.2:c.294C>A
PRKN transcript variant X1 XM_017010908.2:c.855= XM_017010908.2:c.855C>T XM_017010908.2:c.855C>G XM_017010908.2:c.855C>A
PRKN transcript variant X1 XM_017010908.1:c.855= XM_017010908.1:c.855C>T XM_017010908.1:c.855C>G XM_017010908.1:c.855C>A
PRKN transcript variant X2 XM_011535863.2:c.738= XM_011535863.2:c.738C>T XM_011535863.2:c.738C>G XM_011535863.2:c.738C>A
PRKN transcript variant X2 XM_011535863.1:c.738= XM_011535863.1:c.738C>T XM_011535863.1:c.738C>G XM_011535863.1:c.738C>A
PRKN transcript variant X3 XM_024446449.2:c.504= XM_024446449.2:c.504C>T XM_024446449.2:c.504C>G XM_024446449.2:c.504C>A
PRKN transcript variant X3 XM_024446449.1:c.504= XM_024446449.1:c.504C>T XM_024446449.1:c.504C>G XM_024446449.1:c.504C>A
E3 ubiquitin-protein ligase parkin isoform 1 NP_004553.2:p.Pro247= NP_004553.2:p.Pro247= NP_004553.2:p.Pro247= NP_004553.2:p.Pro247=
E3 ubiquitin-protein ligase parkin isoform 2 NP_054642.2:p.Pro219= NP_054642.2:p.Pro219= NP_054642.2:p.Pro219= NP_054642.2:p.Pro219=
E3 ubiquitin-protein ligase parkin isoform 3 NP_054643.2:p.Pro98= NP_054643.2:p.Pro98= NP_054643.2:p.Pro98= NP_054643.2:p.Pro98=
E3 ubiquitin-protein ligase parkin isoform X1 XP_016866397.1:p.Pro285= XP_016866397.1:p.Pro285= XP_016866397.1:p.Pro285= XP_016866397.1:p.Pro285=
E3 ubiquitin-protein ligase parkin isoform X2 XP_011534165.1:p.Pro246= XP_011534165.1:p.Pro246= XP_011534165.1:p.Pro246= XP_011534165.1:p.Pro246=
E3 ubiquitin-protein ligase parkin isoform X3 XP_024302217.1:p.Pro168= XP_024302217.1:p.Pro168= XP_024302217.1:p.Pro168= XP_024302217.1:p.Pro168=
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, 10 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342228258 May 09, 2011 (134)
2 EVA_UK10K_ALSPAC ss1617193523 Apr 01, 2015 (144)
3 EVA_UK10K_TWINSUK ss1660187556 Apr 01, 2015 (144)
4 EVA_EXAC ss1688581046 Apr 01, 2015 (144)
5 HUMAN_LONGEVITY ss2290289503 Dec 20, 2016 (150)
6 GNOMAD ss2736191667 Nov 08, 2017 (151)
7 GNOMAD ss2747742589 Nov 08, 2017 (151)
8 GNOMAD ss2847709123 Nov 08, 2017 (151)
9 EVA ss3824242865 Apr 26, 2020 (154)
10 TOPMED ss4729646512 Apr 27, 2021 (155)
11 TOPMED ss4729646513 Apr 27, 2021 (155)
12 EVA ss5370479074 Oct 14, 2022 (156)
13 EVA ss5935845630 Oct 14, 2022 (156)
14 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 162206934 Oct 12, 2018 (152)
15 ExAC NC_000006.11 - 162206934 Oct 12, 2018 (152)
16 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 247715484 (NC_000006.12:161785901:G:A 7/140250)
Row 247715485 (NC_000006.12:161785901:G:T 2/140250)

- Apr 27, 2021 (155)
17 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 247715484 (NC_000006.12:161785901:G:A 7/140250)
Row 247715485 (NC_000006.12:161785901:G:T 2/140250)

- Apr 27, 2021 (155)
18 gnomAD - Exomes NC_000006.11 - 162206934 Jul 13, 2019 (153)
19 GO Exome Sequencing Project NC_000006.11 - 162206934 Oct 12, 2018 (152)
20 TopMed

Submission ignored due to conflicting rows:
Row 567024070 (NC_000006.12:161785901:G:A 13/264690)
Row 567024071 (NC_000006.12:161785901:G:T 1/264690)

- Apr 27, 2021 (155)
21 TopMed

Submission ignored due to conflicting rows:
Row 567024070 (NC_000006.12:161785901:G:A 13/264690)
Row 567024071 (NC_000006.12:161785901:G:T 1/264690)

- Apr 27, 2021 (155)
22 UK 10K study - Twins NC_000006.11 - 162206934 Oct 12, 2018 (152)
23 ALFA NC_000006.12 - 161785902 Apr 27, 2021 (155)
24 ClinVar RCV002094734.3 Oct 14, 2022 (156)
25 ClinVar RCV002103650.3 Oct 14, 2022 (156)
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
19574174, 8634770, 5347771, 700847, 19574174, ss342228258, ss1617193523, ss1660187556, ss1688581046, ss2736191667, ss2747742589, ss2847709123, ss3824242865, ss5370479074, ss5935845630 NC_000006.11:162206933:G:A NC_000006.12:161785901:G:A (self)
RCV002103650.3, 12973705108, ss2290289503, ss4729646512 NC_000006.12:161785901:G:A NC_000006.12:161785901:G:A (self)
ss5935845630 NC_000006.11:162206933:G:C NC_000006.12:161785901:G:C
RCV002094734.3, 12973705108, ss4729646513 NC_000006.12:161785901:G:T NC_000006.12:161785901: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 rs149749354

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