rs1317538

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000370398.6(KCNQ5):​c.399-64220G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 151,954 control chromosomes in the GnomAD database, including 22,736 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 0.54 ( 22736 hom., cov: 32)

Consequence

KCNQ5
ENST00000370398.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.517
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KCNQ5NM_019842.4 linkuse as main transcriptc.399-64220G>A intron_variant ENST00000370398.6 NP_062816.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KCNQ5ENST00000370398.6 linkuse as main transcriptc.399-64220G>A intron_variant 1 NM_019842.4 ENSP00000359425 P4Q9NR82-1

Frequencies

GnomAD3 genomes
AF:
0.544
AC:
82539
AN:
151836
Hom.:
22719
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.617
Gnomad AMI
AF:
0.543
Gnomad AMR
AF:
0.567
Gnomad ASJ
AF:
0.524
Gnomad EAS
AF:
0.653
Gnomad SAS
AF:
0.497
Gnomad FIN
AF:
0.457
Gnomad MID
AF:
0.579
Gnomad NFE
AF:
0.504
Gnomad OTH
AF:
0.521
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.544
AC:
82623
AN:
151954
Hom.:
22736
Cov.:
32
AF XY:
0.545
AC XY:
40440
AN XY:
74258
show subpopulations
Gnomad4 AFR
AF:
0.617
Gnomad4 AMR
AF:
0.567
Gnomad4 ASJ
AF:
0.524
Gnomad4 EAS
AF:
0.653
Gnomad4 SAS
AF:
0.497
Gnomad4 FIN
AF:
0.457
Gnomad4 NFE
AF:
0.504
Gnomad4 OTH
AF:
0.524
Alfa
AF:
0.490
Hom.:
9490
Bravo
AF:
0.552
Asia WGS
AF:
0.579
AC:
2016
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.26
DANN
Benign
0.51

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1317538; hg19: chr6-73649411; API