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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.

rs1485065718

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:8371380-8371384 (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
delAATT
Variation Type
Indel Insertion and Deletion
Frequency
delAATT=0.000008 (2/264690, TOPMED)
delAATT=0.000008 (2/251492, GnomAD_exome)
delAATT=0.000007 (1/140224, GnomAD) (+ 1 more)
delAATT=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
KRBA2 : Frameshift 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 TAATT=1.00000 T=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 TAATT=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 TAATT=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 TAATT=1.000 T=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 TAATT=1.0000 T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 TAATT=1.000 T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 TAATT=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 TAATT=1.00 T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 TAATT=1.000 T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 TAATT=1.000 T=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 TAATT=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Sub 496 TAATT=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 TAATT=0.999992 delAATT=0.000008
gnomAD - Exomes Global Study-wide 251492 TAATT=0.999992 delAATT=0.000008
gnomAD - Exomes European Sub 135414 TAATT=0.999993 delAATT=0.000007
gnomAD - Exomes Asian Sub 49010 TAATT=1.00000 delAATT=0.00000
gnomAD - Exomes American Sub 34592 TAATT=0.99997 delAATT=0.00003
gnomAD - Exomes African Sub 16256 TAATT=1.00000 delAATT=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10080 TAATT=1.00000 delAATT=0.00000
gnomAD - Exomes Other Sub 6140 TAATT=1.0000 delAATT=0.0000
gnomAD - Genomes Global Study-wide 140224 TAATT=0.999993 delAATT=0.000007
gnomAD - Genomes European Sub 75938 TAATT=1.00000 delAATT=0.00000
gnomAD - Genomes African Sub 42040 TAATT=1.00000 delAATT=0.00000
gnomAD - Genomes American Sub 13646 TAATT=0.99993 delAATT=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3324 TAATT=1.0000 delAATT=0.0000
gnomAD - Genomes East Asian Sub 3126 TAATT=1.0000 delAATT=0.0000
gnomAD - Genomes Other Sub 2150 TAATT=1.0000 delAATT=0.0000
Allele Frequency Aggregator Total Global 14050 TAATT=1.00000 delAATT=0.00000
Allele Frequency Aggregator European Sub 9690 TAATT=1.0000 delAATT=0.0000
Allele Frequency Aggregator African Sub 2898 TAATT=1.0000 delAATT=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 TAATT=1.000 delAATT=0.000
Allele Frequency Aggregator Other Sub 496 TAATT=1.000 delAATT=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 TAATT=1.000 delAATT=0.000
Allele Frequency Aggregator Asian Sub 112 TAATT=1.000 delAATT=0.000
Allele Frequency Aggregator South Asian Sub 98 TAATT=1.00 delAATT=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 17 NC_000017.11:g.8371381_8371384del
GRCh37.p13 chr 17 NC_000017.10:g.8274699_8274702del
Gene: KRBA2, KRAB-A domain containing 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
KRBA2 transcript variant 2 NM_001304947.3:c.-20-997_…

NM_001304947.3:c.-20-997_-20-994del

N/A Intron Variant
KRBA2 transcript variant 1 NM_213597.3:c.152_155del N [AAT] > I [AT] Coding Sequence Variant
KRAB-A domain-containing protein 2 isoform a NP_998762.1:p.Asn51fs N (Asn) > I (Ile) Frameshift 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 TAATT= delAATT
GRCh38.p14 chr 17 NC_000017.11:g.8371380_8371384= NC_000017.11:g.8371381_8371384del
GRCh37.p13 chr 17 NC_000017.10:g.8274698_8274702= NC_000017.10:g.8274699_8274702del
KRBA2 transcript variant 1 NM_213597.3:c.151_155= NM_213597.3:c.152_155del
KRBA2 transcript NM_213597.2:c.151_155= NM_213597.2:c.152_155del
KRAB-A domain-containing protein 2 isoform a NP_998762.1:p.Asn51_Tyr52= NP_998762.1:p.Asn51fs
KRBA2 transcript variant 2 NM_001304947.3:c.-20-994= NM_001304947.3:c.-20-997_-20-994del
KRBA2 transcript variant X2 XM_005256444.1:c.-20-994= XM_005256444.1:c.-20-997_-20-994del
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 ss2742440270 Nov 08, 2017 (151)
2 GNOMAD ss2749688635 Nov 08, 2017 (151)
3 GNOMAD ss2947495269 Nov 08, 2017 (151)
4 TOPMED ss5028849162 Apr 26, 2021 (155)
5 gnomAD - Genomes NC_000017.11 - 8371380 Apr 26, 2021 (155)
6 gnomAD - Exomes NC_000017.10 - 8274698 Jul 13, 2019 (153)
7 TopMed NC_000017.11 - 8371380 Apr 26, 2021 (155)
8 ALFA NC_000017.11 - 8371380 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
11739963, ss2742440270, ss2749688635, ss2947495269 NC_000017.10:8274697:TAAT: NC_000017.11:8371379:TAATT:T (self)
500973358, 244394824, ss5028849162 NC_000017.11:8371379:TAAT: NC_000017.11:8371379:TAATT:T (self)
10172625523 NC_000017.11:8371379:TAATT:T NC_000017.11:8371379:TAATT: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 rs1485065718

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