9-97910241-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016481.5(TRMO):c.785A>C(p.Gln262Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000101 in 1,614,144 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 Uncertain significance (★).
Frequency
Consequence
NM_016481.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRMO | NM_016481.5 | c.785A>C | p.Gln262Pro | missense_variant | 4/5 | ENST00000375119.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRMO | ENST00000375119.8 | c.785A>C | p.Gln262Pro | missense_variant | 4/5 | 1 | NM_016481.5 | P1 | |
TRMO | ENST00000375118.1 | c.347A>C | p.Gln116Pro | missense_variant | 1/2 | 1 | |||
TRMO | ENST00000478126.5 | n.589A>C | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
TRMO | ENST00000375117.8 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152250Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251482Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135912
GnomAD4 exome AF: 0.000109 AC: 159AN: 1461894Hom.: 0 Cov.: 33 AF XY: 0.0000990 AC XY: 72AN XY: 727248
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152250Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74396
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2023 | The c.785A>C (p.Q262P) alteration is located in exon 4 (coding exon 4) of the TRMO gene. This alteration results from a A to C substitution at nucleotide position 785, causing the glutamine (Q) at amino acid position 262 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at