chr1-1512287-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001170535.3(ATAD3A):āc.19A>Cā(p.Ile7Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000659 in 151,652 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (ā ).
Frequency
Consequence
NM_001170535.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATAD3A | NM_001170535.3 | c.19A>C | p.Ile7Leu | missense_variant | 1/16 | ENST00000378756.8 | NP_001164006.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATAD3A | ENST00000378756.8 | c.19A>C | p.Ile7Leu | missense_variant | 1/16 | 1 | NM_001170535.3 | ENSP00000368031 | P1 | |
ATAD3A | ENST00000378755.9 | c.19A>C | p.Ile7Leu | missense_variant | 1/16 | 2 | ENSP00000368030 | |||
ATAD3A | ENST00000672388.1 | n.123A>C | non_coding_transcript_exon_variant | 1/14 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151652Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151652Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74064
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Mar 31, 2022 | Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at