2-70785814-C-A

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.385-175G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 152,080 control chromosomes in the GnomAD database, including 22,990 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.54 (22990 hom., cov: 33)
• Consequence: FIGLA NM_001004311.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 2-70785814-C-A is Benign according to our data. Variant chr2-70785814-C-A is described in ClinVar as [Benign]. Clinvar id is 1292690.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FIGLA	NM_001004311.3	c.385-175G>T		intron_variant		ENST00000332372.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FIGLA	ENST00000332372.6	c.385-175G>T		intron_variant		1	NM_001004311.3	P1

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81530 AN: 151962 Hom.: 22971 Cov.: 33

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.537 AC: 81607 AN: 152080 Hom.: 22990 Cov.: 33 AF XY: 0.546 AC XY: 40565 AN XY: 74322

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.537

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.540

Alfa AF: 0.323 Hom.: 765

Bravo AF: 0.540

Asia WGS AF: 0.651 AC: 2264 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

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	0.41
Dann	Benign	0.75

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: rs7566700; hg19: chr2-71012946;