Variant 6-39315040-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_032115.4(KCNK16):c.892C>T(p.Gln298*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0039 in 1,613,314 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0032 ( 2 hom., cov: 33)

Exomes 𝑓: 0.0040 ( 26 hom. )

Consequence

KCNK16
NM_032115.4 stop_gained

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.438

Variant links:

Genes affected

KCNK16 (HGNC:14464): (potassium two pore domain channel subfamily K member 16) 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 expressed predominantly in the pancreas and is activated at alkaline pH. Several alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Sep 2008]

KCNK16 links:

LOC105375047 (HGNC:):

LOC105375047 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 6-39315040-G-A is Benign according to our data. Variant chr6-39315040-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2656533.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	Protein	UniProt
KCNK16	NM_032115.4 linkuse as main transcript	c.892C>T	p.Gln298*	stop_gained	6/6	NP_115491.1	Q96T55-1
KCNK16	NM_001135107.2 linkuse as main transcript	c.751C>T	p.Gln251*	stop_gained	5/5	NP_001128579.1	Q96T55-5
KCNK16	NM_001363784.1 linkuse as main transcript	c.556C>T	p.Gln186*	stop_gained	6/6	NP_001350713.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	Protein	UniProt
KCNK16	ENST00000373229.9 linkuse as main transcript	c.892C>T	p.Gln298*	stop_gained	6/6	1	ENSP00000362326.5	Q96T55-1
KCNK16	ENST00000373227.8 linkuse as main transcript	c.751C>T	p.Gln251*	stop_gained	5/5	1	ENSP00000362324.4	Q96T55-5
KCNK16	ENST00000425054 linkuse as main transcript	c.*84C>T		3_prime_UTR_variant	5/5	1	ENSP00000391498.2	Q96T55-4
KCNK16	ENST00000507712.5 linkuse as main transcript	c.556C>T	p.Gln186*	stop_gained	6/6	3	ENSP00000423842.1	D6RC57

Frequencies

GnomAD3 genomes

AF:

0.00321

AC:

488

AN:

152214

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000700

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00288

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00476

Gnomad FIN

AF:

0.00536

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00475

Gnomad OTH

AF:

0.00334

GnomAD3 exomes

AF:

0.00385

AC:

965

AN:

250728

Hom.:

AF XY:

0.00402

AC XY:

544

AN XY:

135490

show subpopulations

Gnomad AFR exome

AF:

0.000369

Gnomad AMR exome

AF:

0.00270

Gnomad ASJ exome

AF:

0.000401

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00668

Gnomad FIN exome

AF:

0.00537

Gnomad NFE exome

AF:

0.00453

Gnomad OTH exome

AF:

0.00459

GnomAD4 exome

AF:

0.00397

AC:

5798

AN:

1460982

Hom.:

Cov.:

AF XY:

0.00414

AC XY:

3007

AN XY:

726708

show subpopulations

Gnomad4 AFR exome

AF:

0.000598

Gnomad4 AMR exome

AF:

0.00289

Gnomad4 ASJ exome

AF:

0.000537

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00652

Gnomad4 FIN exome

AF:

0.00569

Gnomad4 NFE exome

AF:

0.00407

Gnomad4 OTH exome

AF:

0.00358

GnomAD4 genome

AF:

0.00320

AC:

487

AN:

152332

Hom.:

Cov.:

AF XY:

0.00338

AC XY:

252

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.000698

Gnomad4 AMR

AF:

0.00288

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00477

Gnomad4 FIN

AF:

0.00536

Gnomad4 NFE

AF:

0.00475

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00410

Hom.:

Bravo

AF:

0.00271

TwinsUK

AF:

0.00297

AC:

ALSPAC

AF:

0.00441

AC:

ESP6500AA

AF:

0.000681

AC:

ESP6500EA

AF:

0.00244

AC:

ExAC

AF:

0.00377

AC:

458

Asia WGS

AF:

0.00202

AC:

AN:

3478

EpiCase

AF:

0.00589

EpiControl

AF:

0.00563

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2022

KCNK16: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.81

CADD

Benign

DANN

Benign

0.89

Eigen

Benign

-0.58

Eigen_PC

Benign

-0.78

FATHMM_MKL

Benign

0.045

Vest4

0.098

GERP RS

-0.34

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over