chr17-30834184-A-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_024857.5(ATAD5):c.103A>T(p.Thr35Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 1,583,100 control chromosomes in the GnomAD database, including 23,021 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_024857.5 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 |
---|---|---|---|---|---|---|---|
ATAD5 | NM_024857.5 | c.103A>T | p.Thr35Ser | missense_variant | 2/23 | ENST00000321990.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATAD5 | ENST00000321990.5 | c.103A>T | p.Thr35Ser | missense_variant | 2/23 | 1 | NM_024857.5 | P1 | |
ATAD5 | ENST00000578295.5 | c.103A>T | p.Thr35Ser | missense_variant | 2/15 | 1 |
Frequencies
GnomAD3 genomes AF: 0.231 AC: 35046AN: 152008Hom.: 6092 Cov.: 32
GnomAD3 exomes AF: 0.166 AC: 37685AN: 226368Hom.: 4490 AF XY: 0.162 AC XY: 19884AN XY: 122976
GnomAD4 exome AF: 0.134 AC: 192342AN: 1430974Hom.: 16893 Cov.: 31 AF XY: 0.137 AC XY: 97023AN XY: 710470
GnomAD4 genome AF: 0.231 AC: 35146AN: 152126Hom.: 6128 Cov.: 32 AF XY: 0.229 AC XY: 17035AN XY: 74386
ClinVar
Submissions by phenotype
ATAD5-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 18, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at