2-70785907-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001004311.3(FIGLA):c.385-268G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 151,960 control chromosomes in the GnomAD database, including 23,055 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.54 (23055 hom., cov: 31)
• Consequence: FIGLA NM_001004311.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.38

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BP6: Variant 2-70785907-C-T is Benign according to our data. Variant chr2-70785907-C-T is described in ClinVar as [Benign]. Clinvar id is 1294027.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FIGLA	NM_001004311.3	c.385-268G>A		intron_variant		ENST00000332372.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FIGLA	ENST00000332372.6	c.385-268G>A		intron_variant		1	NM_001004311.3	P1

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81617 AN: 151842 Hom.: 23036 Cov.: 31

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.537

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.538 AC: 81694 AN: 151960 Hom.: 23055 Cov.: 31 AF XY: 0.547 AC XY: 40601 AN XY: 74242

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.537

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.736

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.541

Alfa AF: 0.386 Hom.: 1442

Bravo AF: 0.542

Asia WGS AF: 0.657 AC: 2285 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 26, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	1.4
Dann	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7566814; hg19: chr2-71013039;