rs719674

chr8-36903466-C-T

Variant summary

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

The NM_001031836.3(KCNU1):c.2010-2242C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 151,992 control chromosomes in the GnomAD database, including 9,682 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 0.34 (9682 hom., cov: 32)
• Consequence: KCNU1 NM_001031836.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

Genes affected

KCNU1 (HGNC:18867): (potassium calcium-activated channel subfamily U member 1) This gene encodes a member of the potassium channel family of proteins. The encoded voltage-gated ion channel allows the outward flow of potassium ions during plasma membrane hyperpolarization in sperm. Opening of this channel may be regulated by calcium ion levels. Homozygous knockout mice that lack the related mouse gene exhibit male sterility. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

LOC105379375 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNU1	NM_001031836.3	c.2010-2242C>T		intron_variant		ENST00000399881.8
LOC105379375	XR_949672.3	n.289-20116G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNU1	ENST00000399881.8	c.2010-2242C>T		intron_variant		2	NM_001031836.3	P1
KCNU1	ENST00000522372.5	c.2010-2242C>T		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52311 AN: 151874 Hom.: 9678 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.344 AC: 52316 AN: 151992 Hom.: 9682 Cov.: 32 AF XY: 0.343 AC XY: 25511 AN XY: 74282

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.367

Alfa AF: 0.365 Hom.: 1308

Bravo AF: 0.346

Asia WGS AF: 0.398 AC: 1383 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.6
Dann	Benign	0.40

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: rs719674; hg19: chr8-36760984;