rs773354073
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_017711.4(GDPD2):c.9G>A(p.Glu3Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000336 in 1,189,441 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_017711.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GDPD2 | ENST00000374382.4 | c.9G>A | p.Glu3Glu | synonymous_variant | Exon 2 of 16 | 1 | NM_017711.4 | ENSP00000363503.3 | ||
GDPD2 | ENST00000453994.6 | c.9G>A | p.Glu3Glu | synonymous_variant | Exon 2 of 17 | 2 | ENSP00000414019.2 | |||
GDPD2 | ENST00000536730.5 | c.-132-361G>A | intron_variant | Intron 1 of 14 | 2 | ENSP00000445982.1 | ||||
GDPD2 | ENST00000538649.5 | c.-28-770G>A | intron_variant | Intron 1 of 13 | 2 | ENSP00000444601.1 |
Frequencies
GnomAD3 genomes AF: 0.00000891 AC: 1AN: 112188Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34348
GnomAD4 exome AF: 0.00000279 AC: 3AN: 1077199Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 348753
GnomAD4 genome AF: 0.00000891 AC: 1AN: 112242Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34412
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at