17-54937167-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005486.3(TOM1L1):c.974G>A(p.Arg325Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000552 in 1,612,888 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 Uncertain significance (★).
Frequency
Consequence
NM_005486.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000265 AC: 4AN: 151158Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000103 AC: 26AN: 251210Hom.: 0 AF XY: 0.0000884 AC XY: 12AN XY: 135776
GnomAD4 exome AF: 0.0000582 AC: 85AN: 1461730Hom.: 0 Cov.: 32 AF XY: 0.0000633 AC XY: 46AN XY: 727158
GnomAD4 genome AF: 0.0000265 AC: 4AN: 151158Hom.: 0 Cov.: 31 AF XY: 0.0000136 AC XY: 1AN XY: 73700
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.974G>A (p.R325Q) alteration is located in exon 10 (coding exon 10) of the TOM1L1 gene. This alteration results from a G to A substitution at nucleotide position 974, causing the arginine (R) at amino acid position 325 to be replaced by a glutamine (Q). 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