17-70130650-A-G

Position:

• chr17-70130650-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_170741.4(KCNJ16):​c.-190-229A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,158 control chromosomes in the GnomAD database, including 1,518 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.13 (1518 hom., cov: 31)
• Consequence: KCNJ16 NM_170741.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.59

Genes affected

KCNJ16 (HGNC:6262): (potassium inwardly rectifying channel subfamily J member 16) Potassium channels are present in most mammalian cells, where they participate in a wide range of physiologic responses. The protein encoded by this gene is an integral membrane protein and inward-rectifier type potassium channel. The encoded protein, which tends to allow potassium to flow into rather than out of a cell, can form heterodimers with two other inward-rectifier type potassium channels. It may function in fluid and pH balance regulation. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Apr 2014]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 17-70130650-A-G is Benign according to our data. Variant chr17-70130650-A-G is described in ClinVar as [Benign]. Clinvar id is 1293328.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNJ16	NM_170741.4	c.-190-229A>G		intron_variant		ENST00000392671.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNJ16	ENST00000392671.6	c.-190-229A>G		intron_variant		2	NM_170741.4	P1

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20532 AN: 152040 Hom.: 1517 Cov.: 31

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.141

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.135 AC: 20540 AN: 152158 Hom.: 1518 Cov.: 31 AF XY: 0.138 AC XY: 10238 AN XY: 74390

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.139

Alfa AF: 0.143 Hom.: 1618

Bravo AF: 0.132

Asia WGS AF: 0.198 AC: 688 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 01, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.22
DANN	Benign	0.38

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: rs998580; hg19: chr17-68126791;