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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.

rs8180682

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:51923938 (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
C>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000423 (112/264690, TOPMED)
A=0.000164 (23/140246, GnomAD)
A=0.00166 (47/28258, 14KJPN) (+ 7 more)
A=0.00161 (27/16760, 8.3KJPN)
A=0.00007 (1/14050, ALFA)
A=0.0006 (4/6404, 1000G_30x)
A=0.0006 (3/5008, 1000G)
A=0.0062 (18/2922, KOREAN)
A=0.0066 (12/1832, Korea1K)
A=0.000 (0/330, HapMap)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PKHD1 : 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 14050 C=0.99993 A=0.00007
European Sub 9690 C=1.0000 A=0.0000
African Sub 2898 C=1.0000 A=0.0000
African Others Sub 114 C=1.000 A=0.000
African American Sub 2784 C=1.0000 A=0.0000
Asian Sub 112 C=0.991 A=0.009
East Asian Sub 86 C=1.00 A=0.00
Other Asian Sub 26 C=0.96 A=0.04
Latin American 1 Sub 146 C=1.000 A=0.000
Latin American 2 Sub 610 C=1.000 A=0.000
South Asian Sub 98 C=1.00 A=0.00
Other Sub 496 C=1.000 A=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
TopMed Global Study-wide 264690 C=0.999577 A=0.000423
gnomAD - Genomes Global Study-wide 140246 C=0.999836 A=0.000164
gnomAD - Genomes European Sub 75950 C=1.00000 A=0.00000
gnomAD - Genomes African Sub 42036 C=1.00000 A=0.00000
gnomAD - Genomes American Sub 13652 C=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3132 C=0.9930 A=0.0070
gnomAD - Genomes Other Sub 2154 C=0.9995 A=0.0005
14KJPN JAPANESE Study-wide 28258 C=0.99834 A=0.00166
8.3KJPN JAPANESE Study-wide 16760 C=0.99839 A=0.00161
Allele Frequency Aggregator Total Global 14050 C=0.99993 A=0.00007
Allele Frequency Aggregator European Sub 9690 C=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2898 C=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 A=0.000
Allele Frequency Aggregator Other Sub 496 C=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 112 C=0.991 A=0.009
Allele Frequency Aggregator South Asian Sub 98 C=1.00 A=0.00
1000Genomes_30x Global Study-wide 6404 C=0.9994 A=0.0006
1000Genomes_30x African Sub 1786 C=1.0000 A=0.0000
1000Genomes_30x Europe Sub 1266 C=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 C=0.9966 A=0.0034
1000Genomes_30x American Sub 980 C=1.000 A=0.000
1000Genomes Global Study-wide 5008 C=0.9994 A=0.0006
1000Genomes African Sub 1322 C=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 C=0.9970 A=0.0030
1000Genomes Europe Sub 1006 C=1.0000 A=0.0000
1000Genomes South Asian Sub 978 C=1.000 A=0.000
1000Genomes American Sub 694 C=1.000 A=0.000
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9938 A=0.0062
Korean Genome Project KOREAN Study-wide 1832 C=0.9934 A=0.0066
HapMap Global Study-wide 330 C=1.000 A=0.000
HapMap African Sub 120 C=1.000 A=0.000
HapMap American Sub 120 C=1.000 A=0.000
HapMap Asian Sub 90 C=1.00 A=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.51923938C>A
GRCh37.p13 chr 6 NC_000006.11:g.51788736C>A
PKHD1 RefSeqGene NG_008753.1:g.168688G>T
Gene: PKHD1, PKHD1 ciliary IPT domain containing fibrocystin/polyductin (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PKHD1 transcript variant 1 NM_138694.4:c.6121+10172G…

NM_138694.4:c.6121+10172G>T

N/A Intron Variant
PKHD1 transcript variant 2 NM_170724.3:c.6121+10172G…

NM_170724.3:c.6121+10172G>T

N/A Intron Variant
PKHD1 transcript variant X1 XM_011514680.4:c.6121+101…

XM_011514680.4:c.6121+10172G>T

N/A Intron Variant
PKHD1 transcript variant X4 XM_011514682.4:c.6121+101…

XM_011514682.4:c.6121+10172G>T

N/A Intron Variant
PKHD1 transcript variant X7 XM_011514683.4:c.5479+101…

XM_011514683.4:c.5479+10172G>T

N/A Intron Variant
PKHD1 transcript variant X8 XM_011514684.4:c.5410+101…

XM_011514684.4:c.5410+10172G>T

N/A Intron Variant
PKHD1 transcript variant X12 XM_011514685.2:c.6121+101…

XM_011514685.2:c.6121+10172G>T

N/A Intron Variant
PKHD1 transcript variant X14 XM_011514686.3:c.6121+101…

XM_011514686.3:c.6121+10172G>T

N/A Intron Variant
PKHD1 transcript variant X15 XM_011514687.2:c.6121+101…

XM_011514687.2:c.6121+10172G>T

N/A Intron Variant
PKHD1 transcript variant X16 XM_011514688.3:c.6121+101…

XM_011514688.3:c.6121+10172G>T

N/A Intron Variant
PKHD1 transcript variant X21 XM_011514690.4:c.196+1017…

XM_011514690.4:c.196+10172G>T

N/A Intron Variant
PKHD1 transcript variant X20 XM_011514691.4:c.196+1017…

XM_011514691.4:c.196+10172G>T

N/A Intron Variant
PKHD1 transcript variant X2 XM_017010944.3:c.6121+101…

XM_017010944.3:c.6121+10172G>T

N/A Intron Variant
PKHD1 transcript variant X3 XM_017010945.3:c.6046+101…

XM_017010945.3:c.6046+10172G>T

N/A Intron Variant
PKHD1 transcript variant X5 XM_017010946.3:c.6121+101…

XM_017010946.3:c.6121+10172G>T

N/A Intron Variant
PKHD1 transcript variant X6 XM_017010947.3:c.5857+101…

XM_017010947.3:c.5857+10172G>T

N/A Intron Variant
PKHD1 transcript variant X9 XM_017010948.3:c.5410+101…

XM_017010948.3:c.5410+10172G>T

N/A Intron Variant
PKHD1 transcript variant X11 XM_017010949.3:c.4261+101…

XM_017010949.3:c.4261+10172G>T

N/A Intron Variant
PKHD1 transcript variant X13 XM_017010950.2:c.6121+101…

XM_017010950.2:c.6121+10172G>T

N/A Intron Variant
PKHD1 transcript variant X17 XM_017010951.2:c.6121+101…

XM_017010951.2:c.6121+10172G>T

N/A Intron Variant
PKHD1 transcript variant X19 XM_017010952.2:c.6121+101…

XM_017010952.2:c.6121+10172G>T

N/A Intron Variant
PKHD1 transcript variant X18 XM_047418895.1:c.6121+101…

XM_047418895.1:c.6121+10172G>T

N/A Intron Variant
PKHD1 transcript variant X10 XR_001743469.2: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 C= A
GRCh38.p14 chr 6 NC_000006.12:g.51923938= NC_000006.12:g.51923938C>A
GRCh37.p13 chr 6 NC_000006.11:g.51788736= NC_000006.11:g.51788736C>A
PKHD1 RefSeqGene NG_008753.1:g.168688= NG_008753.1:g.168688G>T
PKHD1 transcript variant 1 NM_138694.3:c.6121+10172= NM_138694.3:c.6121+10172G>T
PKHD1 transcript variant 1 NM_138694.4:c.6121+10172= NM_138694.4:c.6121+10172G>T
PKHD1 transcript variant 2 NM_170724.2:c.6121+10172= NM_170724.2:c.6121+10172G>T
PKHD1 transcript variant 2 NM_170724.3:c.6121+10172= NM_170724.3:c.6121+10172G>T
PKHD1 transcript variant X1 XM_011514680.4:c.6121+10172= XM_011514680.4:c.6121+10172G>T
PKHD1 transcript variant X4 XM_011514682.4:c.6121+10172= XM_011514682.4:c.6121+10172G>T
PKHD1 transcript variant X7 XM_011514683.4:c.5479+10172= XM_011514683.4:c.5479+10172G>T
PKHD1 transcript variant X8 XM_011514684.4:c.5410+10172= XM_011514684.4:c.5410+10172G>T
PKHD1 transcript variant X12 XM_011514685.2:c.6121+10172= XM_011514685.2:c.6121+10172G>T
PKHD1 transcript variant X14 XM_011514686.3:c.6121+10172= XM_011514686.3:c.6121+10172G>T
PKHD1 transcript variant X15 XM_011514687.2:c.6121+10172= XM_011514687.2:c.6121+10172G>T
PKHD1 transcript variant X16 XM_011514688.3:c.6121+10172= XM_011514688.3:c.6121+10172G>T
PKHD1 transcript variant X21 XM_011514690.4:c.196+10172= XM_011514690.4:c.196+10172G>T
PKHD1 transcript variant X20 XM_011514691.4:c.196+10172= XM_011514691.4:c.196+10172G>T
PKHD1 transcript variant X2 XM_017010944.3:c.6121+10172= XM_017010944.3:c.6121+10172G>T
PKHD1 transcript variant X3 XM_017010945.3:c.6046+10172= XM_017010945.3:c.6046+10172G>T
PKHD1 transcript variant X5 XM_017010946.3:c.6121+10172= XM_017010946.3:c.6121+10172G>T
PKHD1 transcript variant X6 XM_017010947.3:c.5857+10172= XM_017010947.3:c.5857+10172G>T
PKHD1 transcript variant X9 XM_017010948.3:c.5410+10172= XM_017010948.3:c.5410+10172G>T
PKHD1 transcript variant X11 XM_017010949.3:c.4261+10172= XM_017010949.3:c.4261+10172G>T
PKHD1 transcript variant X13 XM_017010950.2:c.6121+10172= XM_017010950.2:c.6121+10172G>T
PKHD1 transcript variant X17 XM_017010951.2:c.6121+10172= XM_017010951.2:c.6121+10172G>T
PKHD1 transcript variant X19 XM_017010952.2:c.6121+10172= XM_017010952.2:c.6121+10172G>T
PKHD1 transcript variant X18 XM_047418895.1:c.6121+10172= XM_047418895.1:c.6121+10172G>T
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#.

19 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss12570627 Aug 27, 2003 (117)
2 SC_SNP ss12797059 Dec 05, 2003 (119)
3 ILLUMINA ss159645872 Dec 01, 2009 (131)
4 SSMP ss653150701 Apr 25, 2013 (138)
5 ILLUMINA ss833156704 Jul 13, 2019 (153)
6 1000GENOMES ss1320153895 Aug 21, 2014 (142)
7 SYSTEMSBIOZJU ss2626354811 Nov 08, 2017 (151)
8 GNOMAD ss2839063728 Nov 08, 2017 (151)
9 EVA ss3765028248 Jul 13, 2019 (153)
10 KRGDB ss3911407136 Apr 26, 2020 (154)
11 KOGIC ss3959042394 Apr 26, 2020 (154)
12 TOPMED ss4703206270 Apr 26, 2021 (155)
13 TOMMO_GENOMICS ss5177525464 Apr 26, 2021 (155)
14 1000G_HIGH_COVERAGE ss5268466217 Oct 13, 2022 (156)
15 EVA ss5365663236 Oct 13, 2022 (156)
16 1000G_HIGH_COVERAGE ss5554378567 Oct 13, 2022 (156)
17 TOMMO_GENOMICS ss5715581507 Oct 13, 2022 (156)
18 YY_MCH ss5807471303 Oct 13, 2022 (156)
19 EVA ss5883842433 Oct 13, 2022 (156)
20 1000Genomes NC_000006.11 - 51788736 Oct 12, 2018 (152)
21 1000Genomes_30x NC_000006.12 - 51923938 Oct 13, 2022 (156)
22 gnomAD - Genomes NC_000006.12 - 51923938 Apr 26, 2021 (155)
23 HapMap NC_000006.12 - 51923938 Apr 26, 2020 (154)
24 KOREAN population from KRGDB NC_000006.11 - 51788736 Apr 26, 2020 (154)
25 Korean Genome Project NC_000006.12 - 51923938 Apr 26, 2020 (154)
26 8.3KJPN NC_000006.11 - 51788736 Apr 26, 2021 (155)
27 14KJPN NC_000006.12 - 51923938 Oct 13, 2022 (156)
28 TopMed NC_000006.12 - 51923938 Apr 26, 2021 (155)
29 ALFA NC_000006.12 - 51923938 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
31943182, 18584530, 35494771, ss653150701, ss833156704, ss1320153895, ss2626354811, ss2839063728, ss3765028248, ss3911407136, ss5177525464, ss5365663236 NC_000006.11:51788735:C:A NC_000006.12:51923937:C:A (self)
41904502, 225387061, 3133302, 15420395, 49418611, 540583828, 8029122542, ss3959042394, ss4703206270, ss5268466217, ss5554378567, ss5715581507, ss5807471303, ss5883842433 NC_000006.12:51923937:C:A NC_000006.12:51923937:C:A (self)
ss12570627, ss12797059, ss159645872 NT_007592.15:51728735:C:A NC_000006.12:51923937:C: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 rs8180682

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