rs144873312
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_138792.4(LEO1):c.893C>T(p.Ala298Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000446 in 1,612,690 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A298A) has been classified as Likely benign.
Frequency
Consequence
NM_138792.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LEO1 | ENST00000299601.10 | c.893C>T | p.Ala298Val | missense_variant | Exon 3 of 12 | 1 | NM_138792.4 | ENSP00000299601.5 | ||
LEO1 | ENST00000315141.5 | c.893C>T | p.Ala298Val | missense_variant | Exon 3 of 10 | 2 | ENSP00000314610.5 | |||
MAPK6 | ENST00000560802.1 | n.178+10132G>A | intron_variant | Intron 1 of 2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152146Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 251072Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135738
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1460426Hom.: 0 Cov.: 29 AF XY: 0.0000413 AC XY: 30AN XY: 726602
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152264Hom.: 0 Cov.: 31 AF XY: 0.0000806 AC XY: 6AN XY: 74448
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at