17-70131194-C-CA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_170741.4(KCNJ16):c.-94+234dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 85,342 control chromosomes in the GnomAD database, including 1,047 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.18 (1047 hom., cov: 21)
• Consequence: KCNJ16 NM_170741.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.33

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 -10 ACMG points.

• BP6: Variant 17-70131194-C-CA is Benign according to our data. Variant chr17-70131194-C-CA is described in ClinVar as [Benign]. Clinvar id is 1275437.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNJ16	NM_170741.4	c.-94+234dup		intron_variant		ENST00000392671.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNJ16	ENST00000392671.6	c.-94+234dup		intron_variant		2	NM_170741.4	P1

Frequencies

GnomAD3 genomes AF: 0.184 AC: 15695 AN: 85340 Hom.: 1044 Cov.: 21

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.233

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.184 AC: 15704 AN: 85342 Hom.: 1047 Cov.: 21 AF XY: 0.187 AC XY: 7619 AN XY: 40748

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.202

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

May 26, 2021

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Computational scores

Source: dbNSFP v4.3

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: rs36047658; hg19: chr17-68127335;