NM_014458.4:c.1477A>T
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 1P and 4B. PP3BS2
The NM_014458.4(KLHL20):c.1477A>T(p.Met493Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000743 in 1,614,100 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M493V) has been classified as Uncertain significance.
Frequency
Consequence
NM_014458.4 missense
Scores
Clinical Significance
Conservation
Publications
- neurodevelopmental disorderInheritance: AD Classification: STRONG Submitted by: Ambry Genetics
- complex neurodevelopmental disorderInheritance: AD Classification: MODERATE Submitted by: G2P
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ACMG classification
Our verdict: Likely_benign. The variant received -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152224Hom.: 0 Cov.: 32 show subpopulations
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461876Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727238 show subpopulations
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74364 show subpopulations
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at