16-84149105-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_178452.6(DNAAF1):āc.223G>Cā(p.Ala75Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,890 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A75T) has been classified as Uncertain significance.
Frequency
Consequence
NM_178452.6 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 | UniProt |
---|---|---|---|---|---|---|---|
DNAAF1 | NM_178452.6 | c.223G>C | p.Ala75Pro | missense_variant | 2/12 | ENST00000378553.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAAF1 | ENST00000378553.10 | c.223G>C | p.Ala75Pro | missense_variant | 2/12 | 1 | NM_178452.6 | P1 | |
DNAAF1 | ENST00000567918.5 | c.223G>C | p.Ala75Pro | missense_variant, NMD_transcript_variant | 2/7 | 1 | |||
DNAAF1 | ENST00000570298.5 | n.377G>C | non_coding_transcript_exon_variant | 2/11 | 2 | ||||
DNAAF1 | ENST00000563093.5 | c.223G>C | p.Ala75Pro | missense_variant, NMD_transcript_variant | 2/11 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152008Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251488Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135920
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461882Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727240
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152008Hom.: 0 Cov.: 29 AF XY: 0.0000404 AC XY: 3AN XY: 74226
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at