rs73937008

Variant names:

• chr2-70785267-A-C
• rs73937008
• NM_001004311.3:c.609+148T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-70785267-A-C
• chr2-70785267-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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]

FIGLA Gene-Disease associations (from GenCC):

• premature ovarian failure 6

  Inheritance: Unknown, AD Classification: MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004311.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FIGLA	NM_001004311.3	MANE Select	c.609+148T>G		intron	N/A	NP_001004311.2	Q6QHK4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FIGLA	ENST00000332372.6	TSL:1 MANE Select	c.609+148T>G		intron	N/A	ENSP00000333097.6	Q6QHK4

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

African (AFR) AF: 0.258 AC: 3724 AN: 14408

American (AMR) AF: 0.138 AC: 2634 AN: 19106

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 4301 AN: 14294

East Asian (EAS) AF: 0.112 AC: 3633 AN: 32454

South Asian (SAS) AF: 0.164 AC: 7007 AN: 42828

European-Finnish (FIN) AF: 0.187 AC: 6846 AN: 36594

Middle Eastern (MID) AF: 0.273 AC: 595 AN: 2182

European-Non Finnish (NFE) AF: 0.170 AC: 62679 AN: 368680

Other (OTH) AF: 0.193 AC: 5679 AN: 29438

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

African (AFR) AF: 0.247 AC: 10256 AN: 41496

American (AMR) AF: 0.174 AC: 2663 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1080 AN: 3462

East Asian (EAS) AF: 0.114 AC: 592 AN: 5188

South Asian (SAS) AF: 0.162 AC: 780 AN: 4818

European-Finnish (FIN) AF: 0.201 AC: 2127 AN: 10592

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12027 AN: 67978

Other (OTH) AF: 0.239 AC: 504 AN: 2108

Alfa AF: 0.160 Hom.: 802

Bravo AF: 0.202

Asia WGS AF: 0.169 AC: 587 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.0
DANN	Benign	0.77
PhyloP100		-0.071
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs73937008; hg19: chr2-71012399;