rs9471058

chr6-39302834-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
KCNK17	NM_031460.4	c.688+1123G>T		intron_variant		ENST00000373231.9
KCNK17	NM_001135111.2	c.688+1123G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNK17	ENST00000373231.9	c.688+1123G>T		intron_variant		1	NM_031460.4	P1
KCNK17	ENST00000453413.2	c.688+1123G>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29453 AN: 151926 Hom.: 3631 Cov.: 32

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

Gnomad4 AFR AF: 0.0478

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.201

Alfa AF: 0.223 Hom.: 1048

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

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

Other links and lift over

dbSNP: rs9471058; hg19: chr6-39270610;