22-35299809-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000411850(TOM1):c.-120G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 1,152,758 control chromosomes in the GnomAD database, including 223,360 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
ENST00000411850 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TOM1 | ENST00000411850 | c.-120G>A | 5_prime_UTR_variant | Exon 1 of 15 | 1 | ENSP00000413697.1 | ||||
TOM1 | ENST00000425375 | c.-120G>A | 5_prime_UTR_variant | Exon 1 of 14 | 2 | ENSP00000394924.1 | ||||
TOM1 | ENST00000456128 | c.-120G>A | 5_prime_UTR_variant | Exon 1 of 10 | 5 | ENSP00000393714.1 |
Frequencies
GnomAD3 genomes AF: 0.508 AC: 77241AN: 152066Hom.: 22684 Cov.: 34
GnomAD4 exome AF: 0.625 AC: 625807AN: 1000574Hom.: 200692 Cov.: 13 AF XY: 0.625 AC XY: 315813AN XY: 505020
GnomAD4 genome AF: 0.507 AC: 77222AN: 152184Hom.: 22668 Cov.: 34 AF XY: 0.507 AC XY: 37724AN XY: 74408
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 53% of patients studied by a panel of primary immunodeficiencies. Number of patients: 50. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at