chr6-39864488-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001201427.2(DAAM2):c.314G>A(p.Arg105His) variant causes a missense change. The variant allele was found at a frequency of 0.00118 in 1,611,824 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R105C) 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 -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DAAM2 | NM_001201427.2 | c.314G>A | p.Arg105His | missense_variant | 4/25 | ENST00000274867.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAAM2 | ENST00000274867.9 | c.314G>A | p.Arg105His | missense_variant | 4/25 | 1 | NM_001201427.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00458 AC: 697AN: 152074Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00172 AC: 425AN: 246724Hom.: 1 AF XY: 0.00135 AC XY: 180AN XY: 133800
GnomAD4 exome AF: 0.000819 AC: 1195AN: 1459632Hom.: 7 Cov.: 31 AF XY: 0.000784 AC XY: 569AN XY: 725962
GnomAD4 genome ? AF: 0.00462 AC: 703AN: 152192Hom.: 5 Cov.: 32 AF XY: 0.00430 AC XY: 320AN XY: 74408
ClinVar
Submissions by phenotype
DAAM2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 24, 2019 | This variant is classified as 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