chrX-101346542-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_004085.4(TIMM8A):c.251C>T(p.Thr84Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000364 in 1,209,829 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 16 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T84T) has been classified as Likely benign.
Frequency
Consequence
NM_004085.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TIMM8A | NM_004085.4 | c.251C>T | p.Thr84Ile | missense_variant | 2/2 | ENST00000372902.4 | |
TIMM8A | NM_001145951.2 | c.*1845C>T | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TIMM8A | ENST00000372902.4 | c.251C>T | p.Thr84Ile | missense_variant | 2/2 | 1 | NM_004085.4 | P1 | |
TIMM8A | ENST00000644112.2 | c.*1845C>T | 3_prime_UTR_variant | 2/2 | |||||
TIMM8A | ENST00000647480.1 | n.768C>T | non_coding_transcript_exon_variant | 2/2 | |||||
TIMM8A | ENST00000645279.1 | c.*445C>T | 3_prime_UTR_variant, NMD_transcript_variant | 3/3 |
Frequencies
GnomAD3 genomes AF: 0.0000357 AC: 4AN: 111928Hom.: 0 Cov.: 23 AF XY: 0.0000586 AC XY: 2AN XY: 34102
GnomAD3 exomes AF: 0.0000545 AC: 10AN: 183503Hom.: 0 AF XY: 0.0000589 AC XY: 4AN XY: 67935
GnomAD4 exome AF: 0.0000364 AC: 40AN: 1097901Hom.: 0 Cov.: 31 AF XY: 0.0000385 AC XY: 14AN XY: 363385
GnomAD4 genome AF: 0.0000357 AC: 4AN: 111928Hom.: 0 Cov.: 23 AF XY: 0.0000586 AC XY: 2AN XY: 34102
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | TIMM8A: PP2, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 29, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at