chr13-105472644-A-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000595812.2(DAOA):c.47A>T(p.His16Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000683 in 1,614,082 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/10 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H16P) has been classified as Likely benign.
Frequency
Consequence
ENST00000595812.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DAOA | NM_172370.5 | c.240A>T | p.Ser80= | synonymous_variant | 4/6 | ENST00000375936.9 | |
DAOA-AS1 | NR_040247.1 | n.506-6224T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAOA | ENST00000375936.9 | c.240A>T | p.Ser80= | synonymous_variant | 4/6 | 1 | NM_172370.5 | P2 | |
DAOA-AS1 | ENST00000448407.1 | n.506-6224T>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00371 AC: 565AN: 152192Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000954 AC: 238AN: 249382Hom.: 4 AF XY: 0.000769 AC XY: 104AN XY: 135294
GnomAD4 exome AF: 0.000368 AC: 538AN: 1461772Hom.: 7 Cov.: 31 AF XY: 0.000329 AC XY: 239AN XY: 727180
GnomAD4 genome AF: 0.00371 AC: 565AN: 152310Hom.: 3 Cov.: 32 AF XY: 0.00330 AC XY: 246AN XY: 74488
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 08, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at