chr17-70100517-T-C

Position:

• chr17-70100517-T-C

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.-299-141T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.885 in 152,234 control chromosomes in the GnomAD database, including 59,746 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.89 (59746 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: KCNJ16 NM_170741.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.696

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]

ENSG00000230258 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 17-70100517-T-C is Benign according to our data. Variant chr17-70100517-T-C is described in ClinVar as [Benign]. Clinvar id is 1270035.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCNJ16	NM_170741.4	c.-299-141T>C		intron_variant		ENST00000392671.6	NP_733937.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNJ16	ENST00000392671.6	c.-299-141T>C		intron_variant		2	NM_170741.4	ENSP00000376439.1

Frequencies

GnomAD3 genomes AF: 0.885 AC: 134674 AN: 152114 Hom.: 59732 Cov.: 32

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.948

Gnomad MID AF: 0.869

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.885 AC: 134747 AN: 152234 Hom.: 59746 Cov.: 32 AF XY: 0.885 AC XY: 65892 AN XY: 74424

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.864

Gnomad4 ASJ AF: 0.905

Gnomad4 EAS AF: 0.963

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.948

Gnomad4 NFE AF: 0.893

Gnomad4 OTH AF: 0.882

Alfa AF: 0.889 Hom.: 99647

Bravo AF: 0.883

Asia WGS AF: 0.861 AC: 2995 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

Apr 09, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.56

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: rs6501375; hg19: chr17-68096658;