chr2-70785088-G-A

Position:

• chr2-70785088-G-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.609+327C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,252 control chromosomes in the GnomAD database, including 22,238 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.53 (22238 hom., cov: 30)
• Consequence: FIGLA NM_001004311.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.67

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=-0.81).
• BP6: Variant 2-70785088-G-A is Benign according to our data. Variant chr2-70785088-G-A is described in ClinVar as [Benign]. Clinvar id is 1183788.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FIGLA	NM_001004311.3	c.609+327C>T		intron_variant		ENST00000332372.6	NP_001004311.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FIGLA	ENST00000332372.6	c.609+327C>T		intron_variant		1	NM_001004311.3	ENSP00000333097	P1

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80219 AN: 151134 Hom.: 22223 Cov.: 30

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.531 AC: 80286 AN: 151252 Hom.: 22238 Cov.: 30 AF XY: 0.541 AC XY: 39948 AN XY: 73880

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.533

Alfa AF: 0.476 Hom.: 2141

Bravo AF: 0.533

Asia WGS AF: 0.567 AC: 1611 AN: 2838

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	-0.81
CADD	Benign	0.88
DANN	Benign	0.64

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: rs6546631; hg19: chr2-71012220;