1-40784236-T-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_004700.4(KCNQ4):c.143T>A(p.Leu48Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000537 in 1,304,006 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 ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004700.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCNQ4 | NM_004700.4 | c.143T>A | p.Leu48Gln | missense_variant | Exon 1 of 14 | ENST00000347132.10 | NP_004691.2 | |
KCNQ4 | NM_172163.3 | c.143T>A | p.Leu48Gln | missense_variant | Exon 1 of 13 | NP_751895.1 | ||
KCNQ4 | XM_047434057.1 | c.143T>A | p.Leu48Gln | missense_variant | Exon 1 of 13 | XP_047290013.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCNQ4 | ENST00000347132.10 | c.143T>A | p.Leu48Gln | missense_variant | Exon 1 of 14 | 1 | NM_004700.4 | ENSP00000262916.6 | ||
KCNQ4 | ENST00000509682.6 | c.143T>A | p.Leu48Gln | missense_variant | Exon 1 of 13 | 5 | ENSP00000423756.2 |
Frequencies
GnomAD3 genomes AF: 0.0000134 AC: 2AN: 148928Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000589 AC: 68AN: 1155078Hom.: 0 Cov.: 30 AF XY: 0.0000533 AC XY: 30AN XY: 562566
GnomAD4 genome AF: 0.0000134 AC: 2AN: 148928Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 1AN XY: 72638
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.143T>A (p.L48Q) alteration is located in exon 1 (coding exon 1) of the KCNQ4 gene. This alteration results from a T to A substitution at nucleotide position 143, causing the leucine (L) at amino acid position 48 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at