chr2-70785267-A-C

Position:

• chr2-70785267-A-C

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+148T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 712,116 control chromosomes in the GnomAD database, including 12,170 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.20 (3183 hom., cov: 32)
  • Exomes 𝑓: 0.17 (8987 hom.)
• Consequence: FIGLA NM_001004311.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0710

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=-0.87).
• BP6: Variant 2-70785267-A-C is Benign according to our data. Variant chr2-70785267-A-C is described in ClinVar as [Benign]. Clinvar id is 1276509.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FIGLA	NM_001004311.3	c.609+148T>G		intron_variant		ENST00000332372.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FIGLA	ENST00000332372.6	c.609+148T>G		intron_variant		1	NM_001004311.3	P1

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30253 AN: 152014 Hom.: 3176 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.233

GnomAD4 exome AF: 0.173 AC: 97098 AN: 559984 Hom.: 8987 AF XY: 0.173 AC XY: 50107 AN XY: 289718

Gnomad4 AFR exome AF: 0.258

Gnomad4 AMR exome AF: 0.138

Gnomad4 ASJ exome AF: 0.301

Gnomad4 EAS exome AF: 0.112

Gnomad4 SAS exome AF: 0.164

Gnomad4 FIN exome AF: 0.187

Gnomad4 NFE exome AF: 0.170

Gnomad4 OTH exome AF: 0.193

GnomAD4 genome AF: 0.199 AC: 30297 AN: 152132 Hom.: 3183 Cov.: 32 AF XY: 0.200 AC XY: 14852 AN XY: 74374

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.239

Alfa AF: 0.133 Hom.: 338

Bravo AF: 0.202

Asia WGS AF: 0.169 AC: 587 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	-0.87
CADD	Benign	6.0
DANN	Benign	0.77

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: rs73937008; hg19: chr2-71012399;