chr6-39856313-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001201427.2(DAAM2):c.11G>A(p.Arg4His) variant causes a missense change. The variant allele was found at a frequency of 0.0000163 in 1,536,218 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R4L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001201427.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DAAM2 | NM_001201427.2 | c.11G>A | p.Arg4His | missense_variant | 2/25 | ENST00000274867.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAAM2 | ENST00000274867.9 | c.11G>A | p.Arg4His | missense_variant | 2/25 | 1 | NM_001201427.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000261 AC: 4AN: 153478Hom.: 0 AF XY: 0.0000244 AC XY: 2AN XY: 82102
GnomAD4 exome AF: 0.0000166 AC: 23AN: 1384022Hom.: 1 Cov.: 31 AF XY: 0.0000176 AC XY: 12AN XY: 683094
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74360
ClinVar
Submissions by phenotype
DAAM2-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 26, 2024 | The DAAM2 c.11G>A variant is predicted to result in the amino acid substitution p.Arg4His. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.030% of alleles in individuals of East Asian descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at