rs2000203
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_019842.4(KCNQ5):c.399-16565G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 699,616 control chromosomes in the GnomAD database, including 120,030 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 0.52 ( 22800 hom., cov: 31)
Exomes 𝑓: 0.57 ( 97230 hom. )
Consequence
KCNQ5
NM_019842.4 intron
NM_019842.4 intron
Scores
1
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.756
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]
KNOP1P4 (HGNC:48922): (lysine rich nucleolar protein 1 pseudogene 4)
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNQ5 | NM_019842.4 | c.399-16565G>A | intron_variant | ENST00000370398.6 | |||
LOC105377855 | XR_007059641.1 | n.302+7246C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNQ5 | ENST00000370398.6 | c.399-16565G>A | intron_variant | 1 | NM_019842.4 | P4 | |||
KNOP1P4 | ENST00000445020.1 | n.1031G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.520 AC: 78934AN: 151872Hom.: 22798 Cov.: 31
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GnomAD4 exome AF: 0.574 AC: 314365AN: 547626Hom.: 97230 Cov.: 3 AF XY: 0.585 AC XY: 175857AN XY: 300356
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GnomAD4 genome ? AF: 0.519 AC: 78948AN: 151990Hom.: 22800 Cov.: 31 AF XY: 0.519 AC XY: 38533AN XY: 74286
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at