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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.

rs775909166

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr14:103699552 (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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000004 (1/264690, TOPMED)
A=0.000004 (1/250678, GnomAD_exome)
A=0.000007 (1/140010, GnomAD) (+ 2 more)
A=0.000008 (1/120528, ExAC)
A=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
XRCC3 : Stop Gained
KLC1 : 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 T=1.00000 A=0.00000
European Sub 9690 T=1.0000 A=0.0000
African Sub 2898 T=1.0000 A=0.0000
African Others Sub 114 T=1.000 A=0.000
African American Sub 2784 T=1.0000 A=0.0000
Asian Sub 112 T=1.000 A=0.000
East Asian Sub 86 T=1.00 A=0.00
Other Asian Sub 26 T=1.00 A=0.00
Latin American 1 Sub 146 T=1.000 A=0.000
Latin American 2 Sub 610 T=1.000 A=0.000
South Asian Sub 98 T=1.00 A=0.00
Other Sub 496 T=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 T=0.999996 A=0.000004
gnomAD - Exomes Global Study-wide 250678 T=0.999996 A=0.000004
gnomAD - Exomes European Sub 134750 T=0.999993 A=0.000007
gnomAD - Exomes Asian Sub 48956 T=1.00000 A=0.00000
gnomAD - Exomes American Sub 34564 T=1.00000 A=0.00000
gnomAD - Exomes African Sub 16218 T=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10068 T=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6122 T=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140010 T=0.999993 A=0.000007
gnomAD - Genomes European Sub 75836 T=1.00000 A=0.00000
gnomAD - Genomes African Sub 41916 T=1.00000 A=0.00000
gnomAD - Genomes American Sub 13654 T=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3320 T=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 T=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 T=0.9995 A=0.0005
ExAC Global Study-wide 120528 T=0.999992 A=0.000008
ExAC Europe Sub 72702 T=0.99999 A=0.00001
ExAC Asian Sub 25110 T=1.00000 A=0.00000
ExAC American Sub 11552 T=1.00000 A=0.00000
ExAC African Sub 10266 T=1.00000 A=0.00000
ExAC Other Sub 898 T=1.000 A=0.000
Allele Frequency Aggregator Total Global 14050 T=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 9690 T=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2898 T=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 T=1.000 A=0.000
Allele Frequency Aggregator Other Sub 496 T=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 T=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 112 T=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 T=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 14 NC_000014.9:g.103699552T>A
GRCh37.p13 chr 14 NC_000014.8:g.104165889T>A
KLC1 RefSeqGene NG_012307.1:g.75365T>A
XRCC3 RefSeqGene NG_011516.1:g.20935A>T
Gene: KLC1, kinesin light chain 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
KLC1 transcript variant 3 NM_001130107.2:c.1782-110…

NM_001130107.2:c.1782-1103T>A

N/A Intron Variant
KLC1 transcript variant 4 NM_001394832.1:c.1924-110…

NM_001394832.1:c.1924-1103T>A

N/A Intron Variant
KLC1 transcript variant 6 NM_001394834.1:c.1897-110…

NM_001394834.1:c.1897-1103T>A

N/A Intron Variant
KLC1 transcript variant 8 NM_001394836.1:c.1857-110…

NM_001394836.1:c.1857-1103T>A

N/A Intron Variant
KLC1 transcript variant 9 NM_001394837.1:c.1849-110…

NM_001394837.1:c.1849-1103T>A

N/A Intron Variant
KLC1 transcript variant 11 NM_001394839.1:c.1830-110…

NM_001394839.1:c.1830-1103T>A

N/A Intron Variant
KLC1 transcript variant 12 NM_001394840.1:c.1822-110…

NM_001394840.1:c.1822-1103T>A

N/A Intron Variant
KLC1 transcript variant 14 NM_001394842.1:c.1779-110…

NM_001394842.1:c.1779-1103T>A

N/A Intron Variant
KLC1 transcript variant 15 NM_001394843.1:c.1776-110…

NM_001394843.1:c.1776-1103T>A

N/A Intron Variant
KLC1 transcript variant 16 NM_001394844.1:c.1755-110…

NM_001394844.1:c.1755-1103T>A

N/A Intron Variant
KLC1 transcript variant 18 NM_001394846.1:c.1726-110…

NM_001394846.1:c.1726-1103T>A

N/A Intron Variant
KLC1 transcript variant 20 NM_001394848.1:c.1699-110…

NM_001394848.1:c.1699-1103T>A

N/A Intron Variant
KLC1 transcript variant 23 NM_001394851.1:c.1645-110…

NM_001394851.1:c.1645-1103T>A

N/A Intron Variant
KLC1 transcript variant 24 NM_001394852.1:c.1624-110…

NM_001394852.1:c.1624-1103T>A

N/A Intron Variant
KLC1 transcript variant 2 NM_182923.4:c.1651-1103T>A N/A Intron Variant
KLC1 transcript variant 5 NM_001394833.1:c. N/A Genic Downstream Transcript Variant
KLC1 transcript variant 7 NM_001394835.1:c. N/A Genic Downstream Transcript Variant
KLC1 transcript variant 10 NM_001394838.1:c. N/A Genic Downstream Transcript Variant
KLC1 transcript variant 13 NM_001394841.1:c. N/A Genic Downstream Transcript Variant
KLC1 transcript variant 17 NM_001394845.1:c. N/A Genic Downstream Transcript Variant
KLC1 transcript variant 19 NM_001394847.1:c. N/A Genic Downstream Transcript Variant
KLC1 transcript variant 21 NM_001394849.1:c. N/A Genic Downstream Transcript Variant
KLC1 transcript variant 22 NM_001394850.1:c. N/A Genic Downstream Transcript Variant
KLC1 transcript variant 25 NM_001394853.1:c. N/A Genic Downstream Transcript Variant
KLC1 transcript variant 26 NM_001394854.1:c. N/A Genic Downstream Transcript Variant
KLC1 transcript variant 27 NM_001394855.1:c. N/A Genic Downstream Transcript Variant
KLC1 transcript variant 28 NM_001394856.1:c. N/A Genic Downstream Transcript Variant
KLC1 transcript variant 29 NM_001394857.1:c. N/A Genic Downstream Transcript Variant
KLC1 transcript variant 30 NM_001394858.1:c. N/A Genic Downstream Transcript Variant
KLC1 transcript variant 31 NM_001394859.1:c. N/A Genic Downstream Transcript Variant
KLC1 transcript variant 32 NM_001394860.1:c. N/A Genic Downstream Transcript Variant
KLC1 transcript variant 1 NM_005552.5:c. N/A Genic Downstream Transcript Variant
Gene: XRCC3, X-ray repair cross complementing 3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
XRCC3 transcript variant 2 NM_005432.4:c.586A>T K [AAG] > * [TAG] Coding Sequence Variant
DNA repair protein XRCC3 NP_005423.1:p.Lys196Ter K (Lys) > * (Ter) Stop Gained
XRCC3 transcript variant 3 NM_001100118.2:c.586A>T K [AAG] > * [TAG] Coding Sequence Variant
DNA repair protein XRCC3 NP_001093588.1:p.Lys196Ter K (Lys) > * (Ter) Stop Gained
XRCC3 transcript variant 1 NM_001100119.2:c.586A>T K [AAG] > * [TAG] Coding Sequence Variant
DNA repair protein XRCC3 NP_001093589.1:p.Lys196Ter K (Lys) > * (Ter) Stop Gained
XRCC3 transcript variant 6 NM_001371232.1:c.586A>T K [AAG] > * [TAG] Coding Sequence Variant
DNA repair protein XRCC3 NP_001358161.1:p.Lys196Ter K (Lys) > * (Ter) Stop Gained
XRCC3 transcript variant 5 NM_001371231.1:c.586A>T K [AAG] > * [TAG] Coding Sequence Variant
DNA repair protein XRCC3 NP_001358160.1:p.Lys196Ter K (Lys) > * (Ter) Stop Gained
XRCC3 transcript variant 4 NM_001371229.1:c.586A>T K [AAG] > * [TAG] Coding Sequence Variant
DNA repair protein XRCC3 NP_001358158.1:p.Lys196Ter K (Lys) > * (Ter) Stop Gained
XRCC3 transcript variant X1 XM_005268046.3:c.586A>T K [AAG] > * [TAG] Coding Sequence Variant
DNA repair protein XRCC3 isoform X1 XP_005268103.1:p.Lys196Ter K (Lys) > * (Ter) Stop Gained
XRCC3 transcript variant X2 XM_047431766.1:c.586A>T K [AAG] > * [TAG] Coding Sequence Variant
DNA repair protein XRCC3 isoform X1 XP_047287722.1:p.Lys196Ter K (Lys) > * (Ter) Stop Gained
XRCC3 transcript variant X3 XM_047431767.1:c.586A>T K [AAG] > * [TAG] Coding Sequence Variant
DNA repair protein XRCC3 isoform X1 XP_047287723.1:p.Lys196Ter K (Lys) > * (Ter) Stop Gained
XRCC3 transcript variant X4 XM_047431768.1:c.586A>T K [AAG] > * [TAG] Coding Sequence Variant
DNA repair protein XRCC3 isoform X1 XP_047287724.1:p.Lys196Ter K (Lys) > * (Ter) Stop Gained
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= A
GRCh38.p14 chr 14 NC_000014.9:g.103699552= NC_000014.9:g.103699552T>A
GRCh37.p13 chr 14 NC_000014.8:g.104165889= NC_000014.8:g.104165889T>A
KLC1 RefSeqGene NG_012307.1:g.75365= NG_012307.1:g.75365T>A
XRCC3 RefSeqGene NG_011516.1:g.20935= NG_011516.1:g.20935A>T
XRCC3 transcript variant 2 NM_005432.4:c.586= NM_005432.4:c.586A>T
XRCC3 transcript variant 2 NM_005432.3:c.586= NM_005432.3:c.586A>T
XRCC3 transcript variant 1 NM_001100119.2:c.586= NM_001100119.2:c.586A>T
XRCC3 transcript variant 1 NM_001100119.1:c.586= NM_001100119.1:c.586A>T
XRCC3 transcript variant 3 NM_001100118.2:c.586= NM_001100118.2:c.586A>T
XRCC3 transcript variant 3 NM_001100118.1:c.586= NM_001100118.1:c.586A>T
XRCC3 transcript variant 5 NM_001371231.1:c.586= NM_001371231.1:c.586A>T
XRCC3 transcript variant 4 NM_001371229.1:c.586= NM_001371229.1:c.586A>T
XRCC3 transcript variant 6 NM_001371232.1:c.586= NM_001371232.1:c.586A>T
XRCC3 transcript variant X1 XM_005268046.3:c.586= XM_005268046.3:c.586A>T
XRCC3 transcript variant X2 XM_005268046.2:c.586= XM_005268046.2:c.586A>T
XRCC3 transcript variant X2 XM_005268046.1:c.586= XM_005268046.1:c.586A>T
XRCC3 transcript variant X3 XM_047431767.1:c.586= XM_047431767.1:c.586A>T
XRCC3 transcript variant X4 XM_047431768.1:c.586= XM_047431768.1:c.586A>T
XRCC3 transcript variant X2 XM_047431766.1:c.586= XM_047431766.1:c.586A>T
DNA repair protein XRCC3 NP_005423.1:p.Lys196= NP_005423.1:p.Lys196Ter
DNA repair protein XRCC3 NP_001093589.1:p.Lys196= NP_001093589.1:p.Lys196Ter
DNA repair protein XRCC3 NP_001093588.1:p.Lys196= NP_001093588.1:p.Lys196Ter
DNA repair protein XRCC3 NP_001358160.1:p.Lys196= NP_001358160.1:p.Lys196Ter
DNA repair protein XRCC3 NP_001358158.1:p.Lys196= NP_001358158.1:p.Lys196Ter
DNA repair protein XRCC3 NP_001358161.1:p.Lys196= NP_001358161.1:p.Lys196Ter
DNA repair protein XRCC3 isoform X1 XP_005268103.1:p.Lys196= XP_005268103.1:p.Lys196Ter
DNA repair protein XRCC3 isoform X1 XP_047287723.1:p.Lys196= XP_047287723.1:p.Lys196Ter
DNA repair protein XRCC3 isoform X1 XP_047287724.1:p.Lys196= XP_047287724.1:p.Lys196Ter
DNA repair protein XRCC3 isoform X1 XP_047287722.1:p.Lys196= XP_047287722.1:p.Lys196Ter
KLC1 transcript variant 3 NM_001130107.1:c.1782-1103= NM_001130107.1:c.1782-1103T>A
KLC1 transcript variant 3 NM_001130107.2:c.1782-1103= NM_001130107.2:c.1782-1103T>A
KLC1 transcript variant 4 NM_001394832.1:c.1924-1103= NM_001394832.1:c.1924-1103T>A
KLC1 transcript variant 6 NM_001394834.1:c.1897-1103= NM_001394834.1:c.1897-1103T>A
KLC1 transcript variant 8 NM_001394836.1:c.1857-1103= NM_001394836.1:c.1857-1103T>A
KLC1 transcript variant 9 NM_001394837.1:c.1849-1103= NM_001394837.1:c.1849-1103T>A
KLC1 transcript variant 11 NM_001394839.1:c.1830-1103= NM_001394839.1:c.1830-1103T>A
KLC1 transcript variant 12 NM_001394840.1:c.1822-1103= NM_001394840.1:c.1822-1103T>A
KLC1 transcript variant 14 NM_001394842.1:c.1779-1103= NM_001394842.1:c.1779-1103T>A
KLC1 transcript variant 15 NM_001394843.1:c.1776-1103= NM_001394843.1:c.1776-1103T>A
KLC1 transcript variant 16 NM_001394844.1:c.1755-1103= NM_001394844.1:c.1755-1103T>A
KLC1 transcript variant 18 NM_001394846.1:c.1726-1103= NM_001394846.1:c.1726-1103T>A
KLC1 transcript variant 20 NM_001394848.1:c.1699-1103= NM_001394848.1:c.1699-1103T>A
KLC1 transcript variant 23 NM_001394851.1:c.1645-1103= NM_001394851.1:c.1645-1103T>A
KLC1 transcript variant 24 NM_001394852.1:c.1624-1103= NM_001394852.1:c.1624-1103T>A
KLC1 transcript variant 2 NM_182923.3:c.1651-1103= NM_182923.3:c.1651-1103T>A
KLC1 transcript variant 2 NM_182923.4:c.1651-1103= NM_182923.4:c.1651-1103T>A
KLC1 transcript variant X1 XM_005267599.1:c.1924-1103= XM_005267599.1:c.1924-1103T>A
KLC1 transcript variant X2 XM_005267600.1:c.*17-1103= XM_005267600.1:c.*17-1103T>A
KLC1 transcript variant X4 XM_005267602.1:c.1897-1103= XM_005267602.1:c.1897-1103T>A
KLC1 transcript variant X5 XM_005267603.1:c.*17-1103= XM_005267603.1:c.*17-1103T>A
KLC1 transcript variant X6 XM_005267604.1:c.1857-1103= XM_005267604.1:c.1857-1103T>A
KLC1 transcript variant X7 XM_005267605.1:c.1849-1103= XM_005267605.1:c.1849-1103T>A
KLC1 transcript variant X8 XM_005267606.1:c.*17-1103= XM_005267606.1:c.*17-1103T>A
KLC1 transcript variant X9 XM_005267607.1:c.1830-1103= XM_005267607.1:c.1830-1103T>A
KLC1 transcript variant X10 XM_005267608.1:c.1825-1103= XM_005267608.1:c.1825-1103T>A
KLC1 transcript variant X11 XM_005267609.1:c.1822-1103= XM_005267609.1:c.1822-1103T>A
KLC1 transcript variant X12 XM_005267610.1:c.*46-1103= XM_005267610.1:c.*46-1103T>A
KLC1 transcript variant X14 XM_005267612.1:c.*17-1103= XM_005267612.1:c.*17-1103T>A
KLC1 transcript variant X15 XM_005267613.1:c.1758-1103= XM_005267613.1:c.1758-1103T>A
KLC1 transcript variant X16 XM_005267614.1:c.1755-1103= XM_005267614.1:c.1755-1103T>A
KLC1 transcript variant X17 XM_005267615.1:c.1726-1103= XM_005267615.1:c.1726-1103T>A
KLC1 transcript variant X18 XM_005267616.1:c.*17-1103= XM_005267616.1:c.*17-1103T>A
KLC1 transcript variant X19 XM_005267617.1:c.1699-1103= XM_005267617.1:c.1699-1103T>A
KLC1 transcript variant X20 XM_005267618.1:c.*17-1103= XM_005267618.1:c.*17-1103T>A
KLC1 transcript variant X26 XM_005267624.1:c.1624-1103= XM_005267624.1:c.1624-1103T>A
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, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1691648406 Apr 01, 2015 (144)
2 GNOMAD ss2740975254 Nov 08, 2017 (151)
3 GNOMAD ss4284426020 Apr 27, 2021 (155)
4 TOPMED ss4983383574 Apr 27, 2021 (155)
5 ExAC NC_000014.8 - 104165889 Oct 12, 2018 (152)
6 gnomAD - Genomes NC_000014.9 - 103699552 Apr 27, 2021 (155)
7 gnomAD - Exomes NC_000014.8 - 104165889 Jul 13, 2019 (153)
8 TopMed NC_000014.9 - 103699552 Apr 27, 2021 (155)
9 ALFA NC_000014.9 - 103699552 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
2007192, 10234617, ss1691648406, ss2740975254 NC_000014.8:104165888:T:A NC_000014.9:103699551:T:A (self)
461889837, 198929233, 3392472934, ss4284426020, ss4983383574 NC_000014.9:103699551:T:A NC_000014.9:103699551:T: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 rs775909166

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