2-70777524-ATTCC-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001004311.3(FIGLA):c.644+109_644+112del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0213 in 1,471,222 control chromosomes in the GnomAD database, including 382 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.016 ( 33 hom., cov: 32)
Exomes 𝑓: 0.022 ( 349 hom. )
Consequence
FIGLA
NM_001004311.3 intron
NM_001004311.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0880
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.
BP6
?
Variant 2-70777524-ATTCC-A is Benign according to our data. Variant chr2-70777524-ATTCC-A is described in ClinVar as [Likely_benign]. Clinvar id is 1207553.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0165 (2509/152306) while in subpopulation NFE AF= 0.0221 (1503/68028). AF 95% confidence interval is 0.0212. There are 33 homozygotes in gnomad4. There are 1322 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 2508 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FIGLA | NM_001004311.3 | c.644+109_644+112del | intron_variant | ENST00000332372.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FIGLA | ENST00000332372.6 | c.644+109_644+112del | intron_variant | 1 | NM_001004311.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0165 AC: 2508AN: 152188Hom.: 33 Cov.: 32
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GnomAD4 exome AF: 0.0219 AC: 28894AN: 1318916Hom.: 349 AF XY: 0.0220 AC XY: 14315AN XY: 650130
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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 | Apr 25, 2020 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at