chr12-7690336-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_020634.3(GDF3):c.637G>A(p.Gly213Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 1,613,536 control chromosomes in the GnomAD database, including 72,974 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 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_020634.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GDF3 | NM_020634.3 | c.637G>A | p.Gly213Arg | missense_variant | 2/2 | ENST00000329913.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GDF3 | ENST00000329913.4 | c.637G>A | p.Gly213Arg | missense_variant | 2/2 | 1 | NM_020634.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.254 AC: 38501AN: 151858Hom.: 5113 Cov.: 31
GnomAD3 exomes AF: 0.261 AC: 65535AN: 251458Hom.: 9257 AF XY: 0.272 AC XY: 36922AN XY: 135906
GnomAD4 exome AF: 0.300 AC: 438995AN: 1461558Hom.: 67854 Cov.: 35 AF XY: 0.302 AC XY: 219579AN XY: 727108
GnomAD4 genome ? AF: 0.254 AC: 38531AN: 151978Hom.: 5120 Cov.: 31 AF XY: 0.253 AC XY: 18782AN XY: 74282
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Klippel-Feil syndrome 3, autosomal dominant Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at