17-70131194-CAAAAAAAA-CAAAAAA

Variant names:

• chr17-70131194-CAA-C
• rs36047658
• NM_170741.4:c.-94+233_-94+234delAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_170741.4(KCNJ16):​c.-94+233_-94+234delAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000432 in 85,714 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.00043 (0 hom., cov: 21)
• Consequence: KCNJ16 NM_170741.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.750

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCNJ16	NM_170741.4	c.-94+233_-94+234delAA		intron_variant	Intron 3 of 3	ENST00000392671.6	NP_733937.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCNJ16	ENST00000392671.6	c.-94+220_-94+221delAA		intron_variant	Intron 3 of 3	2	NM_170741.4	ENSP00000376439.1

Frequencies

GnomAD3 genomes AF: 0.000432 AC: 37 AN: 85712 Hom.: 0 Cov.: 21

Gnomad AFR AF: 0.000205

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000127

Gnomad ASJ AF: 0.000548

Gnomad EAS AF: 0.000280

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00177

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000593

Gnomad OTH AF: 0.000873

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

GnomAD4 genome AF: 0.000432 AC: 37 AN: 85714 Hom.: 0 Cov.: 21 AF XY: 0.000416 AC XY: 17 AN XY: 40906

Gnomad4 AFR AF: 0.000205

Gnomad4 AMR AF: 0.000127

Gnomad4 ASJ AF: 0.000548

Gnomad4 EAS AF: 0.000281

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00177

Gnomad4 NFE AF: 0.000594

Gnomad4 OTH AF: 0.000865

ClinVar

Not reported in ClinVar

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;