rs7923671
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_016204.4(GDF2):c.347-49T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.911 in 1,345,820 control chromosomes in the GnomAD database, including 561,872 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.85 ( 55947 hom., cov: 32)
Exomes 𝑓: 0.92 ( 505925 hom. )
Consequence
GDF2
NM_016204.4 intron
NM_016204.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.417
Genes affected
GDF2 (HGNC:4217): (growth differentiation factor 2) This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate each subunit of the disulfide-linked homodimer. This protein regulates cartilage and bone development, angiogenesis and differentiation of cholinergic central nervous system neurons. Mutations in this gene are associated with hereditary hemorrhagic telangiectasia. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 10-47324792-T-C is Benign according to our data. Variant chr10-47324792-T-C is described in ClinVar as [Benign]. Clinvar id is 674697.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GDF2 | NM_016204.4 | c.347-49T>C | intron_variant | ENST00000581492.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GDF2 | ENST00000581492.3 | c.347-49T>C | intron_variant | 1 | NM_016204.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.849 AC: 129060AN: 152080Hom.: 55917 Cov.: 32
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GnomAD3 exomes AF: 0.891 AC: 198295AN: 222444Hom.: 89028 AF XY: 0.898 AC XY: 108810AN XY: 121106
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GnomAD4 exome AF: 0.919 AC: 1097201AN: 1193622Hom.: 505925 Cov.: 16 AF XY: 0.920 AC XY: 554712AN XY: 603128
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GnomAD4 genome ? AF: 0.848 AC: 129138AN: 152198Hom.: 55947 Cov.: 32 AF XY: 0.851 AC XY: 63338AN XY: 74442
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 16, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at