chr6-39900079-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PVS1_ModeratePM2BP6_Moderate
The ENST00000538976.5(DAAM2):c.2680-1G>A variant causes a splice acceptor change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,601,038 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000538976.5 splice_acceptor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DAAM2 | NM_001201427.2 | c.2682G>A | p.Glu894= | splice_region_variant, synonymous_variant | 23/25 | ENST00000274867.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAAM2 | ENST00000274867.9 | c.2682G>A | p.Glu894= | splice_region_variant, synonymous_variant | 23/25 | 1 | NM_001201427.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152168Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000132 AC: 3AN: 227756Hom.: 0 AF XY: 0.0000163 AC XY: 2AN XY: 122904
GnomAD4 exome AF: 0.0000138 AC: 20AN: 1448752Hom.: 0 Cov.: 30 AF XY: 0.0000139 AC XY: 10AN XY: 719252
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152286Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74462
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 06, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at