chr14-88254564-G-T

Variant names:

• chr14-88254564-G-T
• NM_138317.3:c.402+8638C>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_138317.3(KCNK10):​c.402+8638C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: KCNK10 NM_138317.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668

Genes affected

KCNK10 (HGNC:6273): (potassium two pore domain channel subfamily K member 10) 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, and is stimulated strongly by arachidonic acid and to a lesser degree by membrane stretching, intracellular acidification, and general anaesthetics. Several alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Sep 2008]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCNK10	NM_138317.3	c.402+8638C>A		intron_variant	Intron 2 of 6	ENST00000319231.10	NP_612190.1
KCNK10	NM_138318.3	c.402+8638C>A		intron_variant	Intron 2 of 6		NP_612191.1
KCNK10	NM_021161.5	c.387+8638C>A		intron_variant	Intron 2 of 6		NP_066984.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCNK10	ENST00000319231.10	c.402+8638C>A		intron_variant	Intron 2 of 6	1	NM_138317.3	ENSP00000312811.5
KCNK10	ENST00000312350.9	c.402+8638C>A		intron_variant	Intron 2 of 6	1		ENSP00000310568.5
KCNK10	ENST00000340700.9	c.387+8638C>A		intron_variant	Intron 2 of 6	1		ENSP00000343104.5
KCNK10	ENST00000556282.1	c.351+8638C>A		intron_variant	Intron 2 of 2	4		ENSP00000452587.1

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.34
DANN	Benign	0.63

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr14-88720908;