1-58660011-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001085487.3(MYSM1):c.2473G>A(p.Glu825Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 1,575,666 control chromosomes in the GnomAD database, including 35,092 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt. Synonymous variant affecting the same amino acid position (i.e. E825E) has been classified as Likely benign.
Frequency
Consequence
NM_001085487.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.267 AC: 40489AN: 151764Hom.: 6178 Cov.: 32
GnomAD3 exomes AF: 0.233 AC: 53391AN: 228820Hom.: 6890 AF XY: 0.230 AC XY: 28574AN XY: 124410
GnomAD4 exome AF: 0.192 AC: 273326AN: 1423784Hom.: 28895 Cov.: 28 AF XY: 0.194 AC XY: 137183AN XY: 708410
GnomAD4 genome AF: 0.267 AC: 40556AN: 151882Hom.: 6197 Cov.: 32 AF XY: 0.274 AC XY: 20309AN XY: 74238
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at