17-70131194-C-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Moderate BP6_Moderate

The NM_170741.4(KCNJ16):c.-94+219C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.018 (0 hom., cov: 15)
  • Failed GnomAD Quality Control
• Consequence: KCNJ16 NM_170741.4 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.14

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 Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BP6: Variant 17-70131194-C-A is Benign according to our data. Variant chr17-70131194-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 1317397.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNJ16	NM_170741.4	c.-94+219C>A		intron_variant		ENST00000392671.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNJ16	ENST00000392671.6	c.-94+219C>A		intron_variant		2	NM_170741.4	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 1487 AN: 83864 Hom.: 0 Cov.: 15 FAILED QC

Gnomad AFR AF: 0.00792

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0182

Gnomad ASJ AF: 0.0210

Gnomad EAS AF: 0.00933

Gnomad SAS AF: 0.0167

Gnomad FIN AF: 0.0215

Gnomad MID AF: 0.0217

Gnomad NFE AF: 0.0263

Gnomad OTH AF: 0.0124

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0178 AC: 1489 AN: 83862 Hom.: 0 Cov.: 15 AF XY: 0.0173 AC XY: 695 AN XY: 40122

Gnomad4 AFR AF: 0.00794

Gnomad4 AMR AF: 0.0184

Gnomad4 ASJ AF: 0.0210

Gnomad4 EAS AF: 0.00938

Gnomad4 SAS AF: 0.0168

Gnomad4 FIN AF: 0.0215

Gnomad4 NFE AF: 0.0263

Gnomad4 OTH AF: 0.0123

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 20, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
Cadd	Benign	19
Dann	Benign	0.70

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: rs1251037571; hg19: chr17-68127335;