chr9-97910230-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_016481.5(TRMO):c.796G>A(p.Val266Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000465 in 1,614,198 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely benign (★).
Frequency
Consequence
NM_016481.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRMO | NM_016481.5 | c.796G>A | p.Val266Met | missense_variant | 4/5 | ENST00000375119.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRMO | ENST00000375119.8 | c.796G>A | p.Val266Met | missense_variant | 4/5 | 1 | NM_016481.5 | P1 | |
TRMO | ENST00000375118.1 | c.358G>A | p.Val120Met | missense_variant | 1/2 | 1 | |||
TRMO | ENST00000478126.5 | n.600G>A | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000283 AC: 43AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000179 AC: 45AN: 251486Hom.: 0 AF XY: 0.000199 AC XY: 27AN XY: 135914
GnomAD4 exome AF: 0.000484 AC: 707AN: 1461890Hom.: 0 Cov.: 33 AF XY: 0.000458 AC XY: 333AN XY: 727246
GnomAD4 genome AF: 0.000282 AC: 43AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74480
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 13, 2021 | 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