NM_170741.4:c.-94+232_-94+234dupAAA

Variant names:

• chr17-70131194-C-CAAA
• rs36047658
• NM_170741.4:c.-94+232_-94+234dupAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_170741.4(KCNJ16):​c.-94+232_-94+234dupAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00502 in 85,776 control chromosomes in the GnomAD database, including 5 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0050 (5 hom., cov: 21)
• Consequence: KCNJ16 NM_170741.4 intron
• Clinical Significance: Not reported in ClinVar
• 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 -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00502 (431/85776) while in subpopulation AFR AF= 0.0137 (401/29284). AF 95% confidence interval is 0.0126. There are 5 homozygotes in gnomad4. There are 212 alleles in male gnomad4 subpopulation. Median coverage is 21. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCNJ16	NM_170741.4	c.-94+232_-94+234dupAAA		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+219_-94+220insAAA		intron_variant	Intron 3 of 3	2	NM_170741.4	ENSP00000376439.1

Frequencies

GnomAD3 genomes AF: 0.00502 AC: 431 AN: 85774 Hom.: 5 Cov.: 21

Gnomad AFR AF: 0.0137

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00190

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00196

Gnomad SAS AF: 0.00115

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000846

Gnomad OTH AF: 0.00174

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

GnomAD4 genome AF: 0.00502 AC: 431 AN: 85776 Hom.: 5 Cov.: 21 AF XY: 0.00518 AC XY: 212 AN XY: 40940

Gnomad4 AFR AF: 0.0137

Gnomad4 AMR AF: 0.00190

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00197

Gnomad4 SAS AF: 0.00115

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000847

Gnomad4 OTH AF: 0.00172

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;