1-40819415-T-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_004700.4(KCNQ4):āc.777T>Gā(p.Ala259Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,726 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars). Synonymous variant affecting the same amino acid position (i.e. A259A) has been classified as Benign.
Frequency
Consequence
NM_004700.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCNQ4 | ENST00000347132.10 | c.777T>G | p.Ala259Ala | synonymous_variant | 5/14 | 1 | NM_004700.4 | ENSP00000262916.6 | ||
KCNQ4 | ENST00000509682.6 | c.777T>G | p.Ala259Ala | synonymous_variant | 5/13 | 5 | ENSP00000423756.2 | |||
KCNQ4 | ENST00000443478.3 | c.462T>G | p.Ala154Ala | synonymous_variant | 4/13 | 5 | ENSP00000406735.3 | |||
KCNQ4 | ENST00000506017.1 | n.96T>G | non_coding_transcript_exon_variant | 2/11 | 2 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251388Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135876
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461726Hom.: 0 Cov.: 56 AF XY: 0.00000138 AC XY: 1AN XY: 727180
GnomAD4 genome Cov.: 30
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at