13-105472693-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_172370.5(DAOA):c.281+8T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000684 in 1,591,120 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_172370.5 splice_region, intron
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 |
---|---|---|---|---|---|---|---|
DAOA | NM_172370.5 | c.281+8T>C | splice_region_variant, intron_variant | ENST00000375936.9 | |||
DAOA-AS1 | NR_040247.1 | n.506-6273A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAOA | ENST00000375936.9 | c.281+8T>C | splice_region_variant, intron_variant | 1 | NM_172370.5 | P2 | |||
DAOA-AS1 | ENST00000448407.1 | n.506-6273A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00371 AC: 564AN: 152150Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000985 AC: 230AN: 233398Hom.: 4 AF XY: 0.000783 AC XY: 99AN XY: 126458
GnomAD4 exome AF: 0.000364 AC: 524AN: 1438852Hom.: 7 Cov.: 30 AF XY: 0.000331 AC XY: 236AN XY: 713962
GnomAD4 genome AF: 0.00370 AC: 564AN: 152268Hom.: 3 Cov.: 32 AF XY: 0.00330 AC XY: 246AN XY: 74454
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