rs146973734
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP5BP4BS2_Supporting
The NM_020634.3(GDF3):c.584G>A(p.Arg195Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000148 in 1,614,062 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R195W) has been classified as Likely benign.
Frequency
Consequence
NM_020634.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GDF3 | NM_020634.3 | c.584G>A | p.Arg195Gln | missense_variant | 2/2 | ENST00000329913.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GDF3 | ENST00000329913.4 | c.584G>A | p.Arg195Gln | missense_variant | 2/2 | 1 | NM_020634.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000178 AC: 27AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000191 AC: 48AN: 251474Hom.: 0 AF XY: 0.000191 AC XY: 26AN XY: 135912
GnomAD4 exome AF: 0.000145 AC: 212AN: 1461856Hom.: 2 Cov.: 34 AF XY: 0.000147 AC XY: 107AN XY: 727234
GnomAD4 genome ? AF: 0.000177 AC: 27AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74414
ClinVar
Submissions by phenotype
Isolated microphthalmia 7 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 15, 2010 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at