15-51962485-T-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_138792.4(LEO1):āc.823A>Gā(p.Arg275Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00312 in 1,608,100 control chromosomes in the GnomAD database, including 53 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_138792.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LEO1 | ENST00000299601.10 | c.823A>G | p.Arg275Gly | missense_variant | 3/12 | 1 | NM_138792.4 | ENSP00000299601.5 | ||
LEO1 | ENST00000315141.5 | c.823A>G | p.Arg275Gly | missense_variant | 3/10 | 2 | ENSP00000314610.5 | |||
MAPK6 | ENST00000560802.1 | n.178+10202T>C | intron_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.00550 AC: 837AN: 152250Hom.: 9 Cov.: 31
GnomAD3 exomes AF: 0.00950 AC: 2377AN: 250196Hom.: 33 AF XY: 0.00780 AC XY: 1054AN XY: 135206
GnomAD4 exome AF: 0.00287 AC: 4179AN: 1455732Hom.: 44 Cov.: 28 AF XY: 0.00270 AC XY: 1958AN XY: 724540
GnomAD4 genome AF: 0.00550 AC: 838AN: 152368Hom.: 9 Cov.: 31 AF XY: 0.00726 AC XY: 541AN XY: 74518
ClinVar
Submissions by phenotype
LEO1-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 14, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at