10-47322741-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 1P and 17B. PP3BP6_Very_StrongBP7BS1BS2
The NM_016204.4(GDF2):c.73C>T(p.Leu25Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000224 in 1,609,612 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_016204.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000155 AC: 38AN: 245722Hom.: 0 AF XY: 0.000150 AC XY: 20AN XY: 133656
GnomAD4 exome AF: 0.0000199 AC: 29AN: 1457276Hom.: 0 Cov.: 31 AF XY: 0.0000180 AC XY: 13AN XY: 724170
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74502
ClinVar
Submissions by phenotype
Telangiectasia, hereditary hemorrhagic, type 5 Benign:1
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Cardiovascular phenotype Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at