chr3-49017259-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001009996.3(DALRD3):c.896A>G(p.Gln299Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 1,614,052 control chromosomes in the GnomAD database, including 513,718 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict 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.
Frequency
Consequence
NM_001009996.3 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 |
---|---|---|---|---|---|---|---|
DALRD3 | NM_001009996.3 | c.896A>G | p.Gln299Arg | missense_variant | 5/12 | ENST00000341949.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DALRD3 | ENST00000341949.9 | c.896A>G | p.Gln299Arg | missense_variant | 5/12 | 1 | NM_001009996.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.820 AC: 124692AN: 152070Hom.: 51477 Cov.: 32
GnomAD3 exomes AF: 0.833 AC: 209547AN: 251478Hom.: 88362 AF XY: 0.832 AC XY: 113052AN XY: 135912
GnomAD4 exome AF: 0.792 AC: 1158446AN: 1461864Hom.: 462194 Cov.: 70 AF XY: 0.796 AC XY: 578700AN XY: 727236
GnomAD4 genome ? AF: 0.820 AC: 124799AN: 152188Hom.: 51524 Cov.: 32 AF XY: 0.826 AC XY: 61485AN XY: 74404
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 19, 2019 | This variant is associated with the following publications: (PMID: 31178129, 30389748) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at