rs9471058

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_031460.4(KCNK17):​c.688+1123G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,042 control chromosomes in the GnomAD database, including 3,635 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 0.19 ( 3635 hom., cov: 32)

Consequence

KCNK17
NM_031460.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.284

Publications

9 publications found
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]
KCNK17 Gene-Disease associations (from GenCC):
  • heart conduction disease
    Inheritance: Unknown Classification: LIMITED Submitted by: Genomics England PanelApp

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KCNK17NM_031460.4 linkc.688+1123G>T intron_variant Intron 4 of 4 ENST00000373231.9 NP_113648.2 Q96T54-3
KCNK17NM_001135111.2 linkc.688+1123G>T intron_variant Intron 4 of 5 NP_001128583.1 Q96T54-4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KCNK17ENST00000373231.9 linkc.688+1123G>T intron_variant Intron 4 of 4 1 NM_031460.4 ENSP00000362328.4 Q96T54-3
KCNK17ENST00000453413.2 linkc.688+1123G>T intron_variant Intron 4 of 5 5 ENSP00000401271.2 Q96T54-4

Frequencies

GnomAD3 genomes
AF:
0.194
AC:
29453
AN:
151926
Hom.:
3631
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0478
Gnomad AMI
AF:
0.186
Gnomad AMR
AF:
0.264
Gnomad ASJ
AF:
0.251
Gnomad EAS
AF:
0.381
Gnomad SAS
AF:
0.291
Gnomad FIN
AF:
0.275
Gnomad MID
AF:
0.218
Gnomad NFE
AF:
0.230
Gnomad OTH
AF:
0.199
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.194
AC:
29468
AN:
152042
Hom.:
3635
Cov.:
32
AF XY:
0.198
AC XY:
14732
AN XY:
74302
show subpopulations
African (AFR)
AF:
0.0478
AC:
1984
AN:
41510
American (AMR)
AF:
0.265
AC:
4045
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.251
AC:
873
AN:
3472
East Asian (EAS)
AF:
0.382
AC:
1961
AN:
5134
South Asian (SAS)
AF:
0.290
AC:
1399
AN:
4816
European-Finnish (FIN)
AF:
0.275
AC:
2901
AN:
10554
Middle Eastern (MID)
AF:
0.211
AC:
62
AN:
294
European-Non Finnish (NFE)
AF:
0.230
AC:
15650
AN:
67958
Other (OTH)
AF:
0.201
AC:
424
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1139
2278
3417
4556
5695
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
324
648
972
1296
1620
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.224
Hom.:
1271
Bravo
AF:
0.191
Asia WGS
AF:
0.315
AC:
1097
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
8.5
DANN
Benign
0.55
PhyloP100
-0.28
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs9471058; hg19: chr6-39270610; API