rs75024165
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_016204.4(GDF2):c.911C>T(p.Thr304Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000903 in 1,613,998 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T304T) has been classified as Likely benign.
Frequency
Consequence
NM_016204.4 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 |
---|---|---|---|---|---|---|---|
GDF2 | NM_016204.4 | c.911C>T | p.Thr304Met | missense_variant | 2/2 | ENST00000581492.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GDF2 | ENST00000581492.3 | c.911C>T | p.Thr304Met | missense_variant | 2/2 | 1 | NM_016204.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00484 AC: 736AN: 152164Hom.: 8 Cov.: 33
GnomAD3 exomes AF: 0.00120 AC: 302AN: 251346Hom.: 3 AF XY: 0.000883 AC XY: 120AN XY: 135872
GnomAD4 exome AF: 0.000493 AC: 720AN: 1461716Hom.: 6 Cov.: 32 AF XY: 0.000425 AC XY: 309AN XY: 727164
GnomAD4 genome AF: 0.00484 AC: 737AN: 152282Hom.: 7 Cov.: 33 AF XY: 0.00440 AC XY: 328AN XY: 74470
ClinVar
Submissions by phenotype
Telangiectasia, hereditary hemorrhagic, type 5 Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Sep 28, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 29, 2023 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Oct 11, 2016 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 17, 2019 | - - |
Cardiovascular phenotype Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 05, 2022 | This alteration is classified as 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