chrX-101348670-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_004085.4(TIMM8A):c.-6C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0105 in 1,208,756 control chromosomes in the GnomAD database, including 53 homozygotes. There are 3,990 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004085.4 5_prime_UTR
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TIMM8A | ENST00000372902.4 | c.-6C>T | 5_prime_UTR_variant | Exon 1 of 2 | 1 | NM_004085.4 | ENSP00000361993.3 | |||
TIMM8A | ENST00000644112.2 | c.-6C>T | 5_prime_UTR_variant | Exon 1 of 2 | ENSP00000494385.1 | |||||
TIMM8A | ENST00000645279.1 | n.-6C>T | non_coding_transcript_exon_variant | Exon 1 of 3 | ENSP00000494239.1 | |||||
TIMM8A | ENST00000645279.1 | n.-6C>T | 5_prime_UTR_variant | Exon 1 of 3 | ENSP00000494239.1 |
Frequencies
GnomAD3 genomes AF: 0.00709 AC: 791AN: 111573Hom.: 5 Cov.: 22 AF XY: 0.00636 AC XY: 215AN XY: 33783
GnomAD3 exomes AF: 0.00687 AC: 1257AN: 183064Hom.: 2 AF XY: 0.00694 AC XY: 469AN XY: 67592
GnomAD4 exome AF: 0.0109 AC: 11936AN: 1097125Hom.: 48 Cov.: 33 AF XY: 0.0104 AC XY: 3775AN XY: 362707
GnomAD4 genome AF: 0.00709 AC: 791AN: 111631Hom.: 5 Cov.: 22 AF XY: 0.00635 AC XY: 215AN XY: 33851
ClinVar
Submissions by phenotype
not specified Benign:3
-6C>T in Exon 01 of TIMM8A: This variant is not expected to have clinical signif icance because it has been identified in 1.0% (58/5545) of European American chr omosomes from a broad population by the NHLBI Exome Sequencing Project (http://e vs.gs.washingto -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
- -
not provided Benign:2
- -
- -
Inborn genetic diseases Benign:1
This alteration is classified as 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