chr6-39901459-G-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001201427.2(DAAM2):c.2969G>T(p.Arg990Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00196 in 1,607,480 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R990H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001201427.2 missense
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 |
---|---|---|---|---|---|---|---|
DAAM2 | NM_001201427.2 | c.2969G>T | p.Arg990Leu | missense_variant | 24/25 | ENST00000274867.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAAM2 | ENST00000274867.9 | c.2969G>T | p.Arg990Leu | missense_variant | 24/25 | 1 | NM_001201427.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00147 AC: 223AN: 152100Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00147 AC: 353AN: 239776Hom.: 0 AF XY: 0.00152 AC XY: 198AN XY: 130622
GnomAD4 exome AF: 0.00202 AC: 2933AN: 1455262Hom.: 6 Cov.: 34 AF XY: 0.00193 AC XY: 1400AN XY: 723874
GnomAD4 genome AF: 0.00146 AC: 223AN: 152218Hom.: 1 Cov.: 32 AF XY: 0.00128 AC XY: 95AN XY: 74436
ClinVar
Submissions by phenotype
DAAM2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 24, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at