chr10-19331478-A-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001142308.3(MALRD1):āc.3797A>Cā(p.Asp1266Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 1,549,768 control chromosomes in the GnomAD database, including 282,934 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/16 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001142308.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MALRD1 | NM_001142308.3 | c.3797A>C | p.Asp1266Ala | missense_variant | 24/40 | ENST00000454679.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MALRD1 | ENST00000454679.7 | c.3797A>C | p.Asp1266Ala | missense_variant | 24/40 | 1 | NM_001142308.3 | P1 | |
MALRD1 | ENST00000377266.7 | c.1724A>C | p.Asp575Ala | missense_variant | 10/25 | 5 |
Frequencies
GnomAD3 genomes AF: 0.632 AC: 96008AN: 151802Hom.: 30736 Cov.: 32
GnomAD3 exomes AF: 0.575 AC: 86297AN: 150186Hom.: 25226 AF XY: 0.569 AC XY: 45855AN XY: 80574
GnomAD4 exome AF: 0.598 AC: 836269AN: 1397848Hom.: 252173 Cov.: 43 AF XY: 0.594 AC XY: 409806AN XY: 689442
GnomAD4 genome AF: 0.632 AC: 96086AN: 151920Hom.: 30761 Cov.: 32 AF XY: 0.630 AC XY: 46793AN XY: 74232
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at