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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.

rs1380608539

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:33290379 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000057 (15/264690, TOPMED)
T=0.000004 (1/246786, GnomAD_exome)
T=0.000050 (7/140238, GnomAD) (+ 1 more)
T=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PFDN6 : Synonymous Variant
WDR46 : 2KB Upstream Variant
MIR6834 : 500B Downstream 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 14050 G=1.00000 T=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 G=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 G=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 G=1.000 T=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 G=1.0000 T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 G=1.000 T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 G=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 G=1.00 T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 G=1.000 T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 G=1.000 T=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 G=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Sub 496 G=1.000 T=0.000 1.0 0.0 0.0 N/A


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=0.999943 T=0.000057
gnomAD - Exomes Global Study-wide 246786 G=0.999996 T=0.000004
gnomAD - Exomes European Sub 133092 G=1.000000 T=0.000000
gnomAD - Exomes Asian Sub 48036 G=1.00000 T=0.00000
gnomAD - Exomes American Sub 33880 G=0.99997 T=0.00003
gnomAD - Exomes African Sub 16194 G=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 9582 G=1.0000 T=0.0000
gnomAD - Exomes Other Sub 6002 G=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 140238 G=0.999950 T=0.000050
gnomAD - Genomes European Sub 75936 G=1.00000 T=0.00000
gnomAD - Genomes African Sub 42022 G=0.99983 T=0.00017
gnomAD - Genomes American Sub 13668 G=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 G=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 14050 G=1.00000 T=0.00000
Allele Frequency Aggregator European Sub 9690 G=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2898 G=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 T=0.000
Allele Frequency Aggregator Other Sub 496 G=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 T=0.00
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.33290379G>T
GRCh37.p13 chr 6 NC_000006.11:g.33258156G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.4701864G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.4701970G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.4484803G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.4490399G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.4533897G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.4539482G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.4726315G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.4731900G>T
Gene: WDR46, WD repeat domain 46 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
WDR46 transcript variant 2 NM_001164267.2:c. N/A Upstream Transcript Variant
WDR46 transcript variant 1 NM_005452.6:c. N/A Upstream Transcript Variant
WDR46 transcript variant X1 XM_047419523.1:c. N/A Upstream Transcript Variant
WDR46 transcript variant X2 XM_047419524.1:c. N/A Upstream Transcript Variant
Gene: PFDN6, prefoldin subunit 6 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PFDN6 transcript variant 4 NM_001265596.1:c.189G>T V [GTG] > V [GTT] Coding Sequence Variant
prefoldin subunit 6 NP_001252525.1:p.Val63= V (Val) > V (Val) Synonymous Variant
PFDN6 transcript variant 3 NM_001265595.2:c.189G>T V [GTG] > V [GTT] Coding Sequence Variant
prefoldin subunit 6 NP_001252524.1:p.Val63= V (Val) > V (Val) Synonymous Variant
PFDN6 transcript variant 1 NM_001185181.3:c.189G>T V [GTG] > V [GTT] Coding Sequence Variant
prefoldin subunit 6 NP_001172110.1:p.Val63= V (Val) > V (Val) Synonymous Variant
PFDN6 transcript variant 2 NM_014260.4:c.189G>T V [GTG] > V [GTT] Coding Sequence Variant
prefoldin subunit 6 NP_055075.1:p.Val63= V (Val) > V (Val) Synonymous Variant
PFDN6 transcript variant X1 XM_047418077.1:c.189G>T V [GTG] > V [GTT] Coding Sequence Variant
prefoldin subunit 6 isoform X1 XP_047274033.1:p.Val63= V (Val) > V (Val) Synonymous Variant
Gene: MIR6834, microRNA 6834 (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
MIR6834 transcript NR_106892.1:n. N/A Downstream Transcript 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= T
GRCh38.p14 chr 6 NC_000006.12:g.33290379= NC_000006.12:g.33290379G>T
GRCh37.p13 chr 6 NC_000006.11:g.33258156= NC_000006.11:g.33258156G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.4701864= NT_113891.3:g.4701864G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.4701970= NT_113891.2:g.4701970G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.4484803= NT_167248.2:g.4484803G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.4490399= NT_167248.1:g.4490399G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.4533897= NT_167245.2:g.4533897G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.4539482= NT_167245.1:g.4539482G>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.4726315= NT_167247.2:g.4726315G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.4731900= NT_167247.1:g.4731900G>T
PFDN6 transcript variant 2 NM_014260.4:c.189= NM_014260.4:c.189G>T
PFDN6 transcript variant 2 NM_014260.3:c.189= NM_014260.3:c.189G>T
PFDN6 transcript variant 1 NM_001185181.3:c.189= NM_001185181.3:c.189G>T
PFDN6 transcript variant 1 NM_001185181.2:c.189= NM_001185181.2:c.189G>T
PFDN6 transcript variant 3 NM_001265595.1:c.189= NM_001265595.1:c.189G>T
PFDN6 transcript variant 3 NM_001265595.2:c.189= NM_001265595.2:c.189G>T
PFDN6 transcript variant X1 XM_047418077.1:c.189= XM_047418077.1:c.189G>T
PFDN6 transcript variant 4 NM_001265596.1:c.189= NM_001265596.1:c.189G>T
prefoldin subunit 6 NP_055075.1:p.Val63= NP_055075.1:p.Val63=
prefoldin subunit 6 NP_001172110.1:p.Val63= NP_001172110.1:p.Val63=
prefoldin subunit 6 NP_001252524.1:p.Val63= NP_001252524.1:p.Val63=
prefoldin subunit 6 isoform X1 XP_047274033.1:p.Val63= XP_047274033.1:p.Val63=
prefoldin subunit 6 NP_001252525.1:p.Val63= NP_001252525.1:p.Val63=
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#.

4 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2735707925 Nov 08, 2017 (151)
2 GNOMAD ss2747599762 Nov 08, 2017 (151)
3 GNOMAD ss2837564621 Nov 08, 2017 (151)
4 TOPMED ss4698709417 Apr 26, 2021 (155)
5 gnomAD - Genomes NC_000006.12 - 33290379 Apr 26, 2021 (155)
6 gnomAD - Exomes NC_000006.11 - 33258156 Jul 13, 2019 (153)
7 TopMed NC_000006.12 - 33290379 Apr 26, 2021 (155)
8 ALFA NC_000006.12 - 33290379 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
4849623, ss2735707925, ss2747599762, ss2837564621 NC_000006.11:33258155:G:T NC_000006.12:33290378:G:T (self)
221545790, 536086975, 4183253238, ss4698709417 NC_000006.12:33290378:G:T NC_000006.12:33290378: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 rs1380608539

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.post820+afb47a3d