9-97910061-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.965G>A(p.Arg322His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,252 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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRMO | ENST00000375119.8 | c.965G>A | p.Arg322His | missense_variant | Exon 4 of 5 | 1 | NM_016481.5 | ENSP00000364260.3 | ||
TRMO | ENST00000375118.1 | c.527G>A | p.Arg176His | missense_variant | Exon 1 of 2 | 1 | ENSP00000364259.1 | |||
TRMO | ENST00000478126.5 | n.769G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 | |||||
TRMO | ENST00000375117.8 | c.*585G>A | downstream_gene_variant | 3 | ENSP00000364258.4 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251112Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135718
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1460938Hom.: 0 Cov.: 33 AF XY: 0.0000151 AC XY: 11AN XY: 726610
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74476
ClinVar
Submissions by phenotype
not specified Benign:1
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