rs2758912

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_031460.4(KCNK17):​c.353-2851T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,966 control chromosomes in the GnomAD database, including 25,326 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.56 ( 25326 hom., cov: 32)

Consequence

KCNK17
NM_031460.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.41
Variant links:
Genes affected
KCNK17 (HGNC:14465): (potassium two pore domain channel subfamily K member 17) The protein encoded by this gene belongs to the family of potassium channel proteins containing two pore-forming P domains. This channel is an open rectifier which primarily passes outward current under physiological K+ concentrations. This gene is activated at alkaline pH. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KCNK17NM_031460.4 linkc.353-2851T>C intron_variant Intron 2 of 4 ENST00000373231.9 NP_113648.2 Q96T54-3
KCNK17NM_001135111.2 linkc.353-2851T>C intron_variant Intron 2 of 5 NP_001128583.1 Q96T54-4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KCNK17ENST00000373231.9 linkc.353-2851T>C intron_variant Intron 2 of 4 1 NM_031460.4 ENSP00000362328.4 Q96T54-3
KCNK17ENST00000503878.1 linkn.458-2851T>C intron_variant Intron 2 of 2 1
KCNK17ENST00000453413.2 linkc.353-2851T>C intron_variant Intron 2 of 5 5 ENSP00000401271.2 Q96T54-4

Frequencies

GnomAD3 genomes
AF:
0.564
AC:
85697
AN:
151846
Hom.:
25267
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.743
Gnomad AMI
AF:
0.427
Gnomad AMR
AF:
0.593
Gnomad ASJ
AF:
0.468
Gnomad EAS
AF:
0.485
Gnomad SAS
AF:
0.454
Gnomad FIN
AF:
0.552
Gnomad MID
AF:
0.424
Gnomad NFE
AF:
0.473
Gnomad OTH
AF:
0.536
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.565
AC:
85822
AN:
151966
Hom.:
25326
Cov.:
32
AF XY:
0.565
AC XY:
41990
AN XY:
74254
show subpopulations
Gnomad4 AFR
AF:
0.743
Gnomad4 AMR
AF:
0.594
Gnomad4 ASJ
AF:
0.468
Gnomad4 EAS
AF:
0.485
Gnomad4 SAS
AF:
0.454
Gnomad4 FIN
AF:
0.552
Gnomad4 NFE
AF:
0.473
Gnomad4 OTH
AF:
0.540
Alfa
AF:
0.485
Hom.:
37334
Bravo
AF:
0.579
Asia WGS
AF:
0.498
AC:
1733
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.57
DANN
Benign
0.82

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2758912; hg19: chr6-39275282; API