rs254285
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005260.7(GDF9):c.398-39G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.885 in 1,531,450 control chromosomes in the GnomAD database, including 604,352 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.89 ( 60600 hom., cov: 30)
Exomes 𝑓: 0.88 ( 543752 hom. )
Consequence
GDF9
NM_005260.7 intron
NM_005260.7 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.469
Genes affected
GDF9 (HGNC:4224): (growth differentiation factor 9) 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 ovarian function. Reduced expression of this gene may be associated with polycystic ovary syndrome and mutations in this gene may be more common in mothers of dizygotic twins. [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=-0.83).
BP6
?
Variant 5-132862595-C-G is Benign according to our data. Variant chr5-132862595-C-G is described in ClinVar as [Benign]. Clinvar id is 1232056.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GDF9 | NM_005260.7 | c.398-39G>C | intron_variant | ENST00000687138.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GDF9 | ENST00000687138.1 | c.398-39G>C | intron_variant | NM_005260.7 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.887 AC: 134830AN: 151984Hom.: 60544 Cov.: 30
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GnomAD3 exomes AF: 0.828 AC: 191959AN: 231764Hom.: 81738 AF XY: 0.840 AC XY: 106908AN XY: 127232
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GnomAD4 exome AF: 0.884 AC: 1219690AN: 1379350Hom.: 543752 Cov.: 22 AF XY: 0.886 AC XY: 612272AN XY: 690864
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GnomAD4 genome ? AF: 0.887 AC: 134945AN: 152100Hom.: 60600 Cov.: 30 AF XY: 0.878 AC XY: 65219AN XY: 74310
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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 26, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at