chr17-30834499-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_024857.5(ATAD5):c.418G>A(p.Asp140Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00332 in 1,584,994 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_024857.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATAD5 | NM_024857.5 | c.418G>A | p.Asp140Asn | missense_variant | 2/23 | ENST00000321990.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATAD5 | ENST00000321990.5 | c.418G>A | p.Asp140Asn | missense_variant | 2/23 | 1 | NM_024857.5 | P1 | |
ATAD5 | ENST00000578295.5 | c.418G>A | p.Asp140Asn | missense_variant | 2/15 | 1 | |||
ENST00000580873.1 | n.464C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00221 AC: 336AN: 152152Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00252 AC: 568AN: 224986Hom.: 2 AF XY: 0.00240 AC XY: 293AN XY: 121992
GnomAD4 exome AF: 0.00344 AC: 4929AN: 1432724Hom.: 7 Cov.: 34 AF XY: 0.00332 AC XY: 2366AN XY: 712346
GnomAD4 genome ? AF: 0.00221 AC: 336AN: 152270Hom.: 1 Cov.: 32 AF XY: 0.00189 AC XY: 141AN XY: 74444
ClinVar
Submissions by phenotype
ATAD5-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 02, 2020 | This variant is classified as likely 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