chr2-70787476-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001004311.3(FIGLA):c.384+173A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00379 in 152,362 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0038 ( 3 hom., cov: 32)
Consequence
FIGLA
NM_001004311.3 intron
NM_001004311.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.478
Genes affected
FIGLA (HGNC:24669): (folliculogenesis specific bHLH transcription factor) This gene encodes a protein that functions in postnatal oocyte-specific gene expression. The protein is a basic helix-loop-helix transcription factor that regulates multiple oocyte-specific genes, including genes involved in folliculogenesis and those that encode the zona pellucida. Mutations in this gene cause premature ovarian failure type 6. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 2-70787476-T-C is Benign according to our data. Variant chr2-70787476-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1200839.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 576 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FIGLA | NM_001004311.3 | c.384+173A>G | intron_variant | ENST00000332372.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FIGLA | ENST00000332372.6 | c.384+173A>G | intron_variant | 1 | NM_001004311.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00378 AC: 576AN: 152244Hom.: 3 Cov.: 32
GnomAD3 genomes
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576
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152244
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00379 AC: 577AN: 152362Hom.: 3 Cov.: 32 AF XY: 0.00336 AC XY: 250AN XY: 74506
GnomAD4 genome
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577
AN:
152362
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32
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250
AN XY:
74506
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 14, 2019 | - - |
Computational scores
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Name
Calibrated prediction
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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