8-132480483-TCGCCGCCGC-TCGCCGC

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_004519.4(KCNQ3):​c.47_49delGCG​(p.Gly16del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000113 in 1,063,162 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.000011 ( 0 hom. )

Consequence

KCNQ3
NM_004519.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.552
Variant links:
Genes affected
KCNQ3 (HGNC:6297): (potassium voltage-gated channel subfamily Q member 3) This gene encodes a protein that functions in the regulation of neuronal excitability. The encoded protein forms an M-channel by associating with the products of the related KCNQ2 or KCNQ5 genes, which both encode integral membrane proteins. M-channel currents are inhibited by M1 muscarinic acetylcholine receptors and are activated by retigabine, a novel anti-convulsant drug. Defects in this gene are a cause of benign familial neonatal convulsions type 2 (BFNC2), also known as epilepsy, benign neonatal type 2 (EBN2). Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2014]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAdExome4 at 12 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KCNQ3NM_004519.4 linkc.47_49delGCG p.Gly16del disruptive_inframe_deletion 1/15 ENST00000388996.10 NP_004510.1 O43525-1
KCNQ3XM_047421769.1 linkc.47_49delGCG p.Gly16del disruptive_inframe_deletion 1/15 XP_047277725.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KCNQ3ENST00000388996.10 linkc.47_49delGCG p.Gly16del disruptive_inframe_deletion 1/151 NM_004519.4 ENSP00000373648.3 O43525-1
KCNQ3ENST00000519445.5 linkc.47_49delGCG p.Gly16del disruptive_inframe_deletion 1/155 ENSP00000428790.1 E7ET42

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.0000113
AC:
12
AN:
1063162
Hom.:
0
AF XY:
0.0000157
AC XY:
8
AN XY:
508152
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.000160
Gnomad4 EAS exome
AF:
0.0000430
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000876
Gnomad4 OTH exome
AF:
0.0000241
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs981093917; hg19: chr8-133492730; API