rs16882712

chr6-72705006-G-A

Variant summary

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

The NM_019842.4(KCNQ5):c.398+82419G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,062 control chromosomes in the GnomAD database, including 1,488 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 0.10 (1488 hom., cov: 32)
• Consequence: KCNQ5 NM_019842.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.973

Genes affected

KCNQ5 (HGNC:6299): (potassium voltage-gated channel subfamily Q member 5) This gene is a member of the KCNQ potassium channel gene family that is differentially expressed in subregions of the brain and in skeletal muscle. The protein encoded by this gene yields currents that activate slowly with depolarization and can form heteromeric channels with the protein encoded by the KCNQ3 gene. Currents expressed from this protein have voltage dependences and inhibitor sensitivities in common with M-currents. They are also inhibited by M1 muscarinic receptor activation. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNQ5	NM_019842.4	c.398+82419G>A		intron_variant		ENST00000370398.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNQ5	ENST00000370398.6	c.398+82419G>A		intron_variant		1	NM_019842.4	P4

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15889 AN: 151944 Hom.: 1483 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0693

Gnomad ASJ AF: 0.0612

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0156

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.0517

Gnomad OTH AF: 0.0903

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

GnomAD4 genome AF: 0.105 AC: 15926 AN: 152062 Hom.: 1488 Cov.: 32 AF XY: 0.101 AC XY: 7486 AN XY: 74326

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.0691

Gnomad4 ASJ AF: 0.0612

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0150

Gnomad4 FIN AF: 0.0440

Gnomad4 NFE AF: 0.0517

Gnomad4 OTH AF: 0.0899

Alfa AF: 0.0807 Hom.: 149

Bravo AF: 0.115

Asia WGS AF: 0.0290 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	5.7
Dann	Benign	0.67

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: rs16882712; hg19: chr6-73414730;