rs16891904

Positions:

• chr6-39320314-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001135106.2(KCNK16):​c.214-1181C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0449 in 152,178 control chromosomes in the GnomAD database, including 240 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.045 (240 hom., cov: 33)
• Consequence: KCNK16 NM_001135106.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

Genes affected

KCNK16 (HGNC:14464): (potassium two pore domain channel subfamily K member 16) The protein encoded by this gene belongs to the family of potassium channel proteins containing two pore-forming P domains. This channel is an open rectifier which primarily passes outward current under physiological K+ concentrations. This gene is expressed predominantly in the pancreas and is activated at alkaline pH. Several alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Sep 2008]

LOC105375047 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCNK16	NM_001135106.2	c.214-1181C>T		intron_variant		ENST00000437525.3	NP_001128578.1
LOC105375047	XR_926774.3	n.269+6090G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNK16	ENST00000437525.3	c.214-1181C>T		intron_variant		1	NM_001135106.2	ENSP00000415375	P1

Frequencies

GnomAD3 genomes AF: 0.0448 AC: 6816 AN: 152060 Hom.: 238 Cov.: 33

Gnomad AFR AF: 0.0865

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0213

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.00773

Gnomad SAS AF: 0.0236

Gnomad FIN AF: 0.0622

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0281

Gnomad OTH AF: 0.0302

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

GnomAD4 genome AF: 0.0449 AC: 6834 AN: 152178 Hom.: 240 Cov.: 33 AF XY: 0.0459 AC XY: 3417 AN XY: 74402

Gnomad4 AFR AF: 0.0867

Gnomad4 AMR AF: 0.0212

Gnomad4 ASJ AF: 0.0187

Gnomad4 EAS AF: 0.00775

Gnomad4 SAS AF: 0.0232

Gnomad4 FIN AF: 0.0622

Gnomad4 NFE AF: 0.0281

Gnomad4 OTH AF: 0.0299

Alfa AF: 0.0366 Hom.: 47

Bravo AF: 0.0437

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.41

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: rs16891904; hg19: chr6-39288090;