chr3-140688418-C-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152616.5(TRIM42):c.1736C>A(p.Ala579Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 1,613,836 control chromosomes in the GnomAD database, including 243,886 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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_152616.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIM42 | NM_152616.5 | c.1736C>A | p.Ala579Glu | missense_variant | 3/5 | ENST00000286349.4 | NP_689829.3 | |
TRIM42 | XM_011512740.4 | c.1736C>A | p.Ala579Glu | missense_variant | 3/5 | XP_011511042.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIM42 | ENST00000286349.4 | c.1736C>A | p.Ala579Glu | missense_variant | 3/5 | 1 | NM_152616.5 | ENSP00000286349.3 |
Frequencies
GnomAD3 genomes AF: 0.482 AC: 73251AN: 151872Hom.: 18634 Cov.: 32
GnomAD3 exomes AF: 0.519 AC: 130180AN: 251052Hom.: 34497 AF XY: 0.521 AC XY: 70752AN XY: 135720
GnomAD4 exome AF: 0.552 AC: 806223AN: 1461846Hom.: 225235 Cov.: 70 AF XY: 0.549 AC XY: 399119AN XY: 727228
GnomAD4 genome AF: 0.482 AC: 73297AN: 151990Hom.: 18651 Cov.: 32 AF XY: 0.482 AC XY: 35823AN XY: 74270
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at