chr14-103534691-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_152307.3(TRMT61A):c.740C>T(p.Pro247Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000224 in 1,608,852 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_152307.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRMT61A | NM_152307.3 | c.740C>T | p.Pro247Leu | missense_variant | Exon 4 of 4 | ENST00000389749.9 | NP_689520.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000377 AC: 9AN: 238648Hom.: 0 AF XY: 0.0000152 AC XY: 2AN XY: 131264
GnomAD4 exome AF: 0.0000206 AC: 30AN: 1456480Hom.: 0 Cov.: 31 AF XY: 0.0000207 AC XY: 15AN XY: 724742
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152372Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74512
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