chr2-70777969-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001004311.3(FIGLA):​c.610-298G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,026 control chromosomes in the GnomAD database, including 14,871 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.43 ( 14871 hom., cov: 32)

Consequence

FIGLA
NM_001004311.3 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.08
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 2-70777969-C-G is Benign according to our data. Variant chr2-70777969-C-G is described in ClinVar as [Benign]. Clinvar id is 1183680.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
FIGLANM_001004311.3 linkuse as main transcriptc.610-298G>C intron_variant ENST00000332372.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FIGLAENST00000332372.6 linkuse as main transcriptc.610-298G>C intron_variant 1 NM_001004311.3 P1

Frequencies

GnomAD3 genomes
AF:
0.425
AC:
64614
AN:
151908
Hom.:
14871
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.277
Gnomad AMI
AF:
0.471
Gnomad AMR
AF:
0.507
Gnomad ASJ
AF:
0.509
Gnomad EAS
AF:
0.737
Gnomad SAS
AF:
0.564
Gnomad FIN
AF:
0.593
Gnomad MID
AF:
0.532
Gnomad NFE
AF:
0.431
Gnomad OTH
AF:
0.467
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.425
AC:
64641
AN:
152026
Hom.:
14871
Cov.:
32
AF XY:
0.440
AC XY:
32695
AN XY:
74294
show subpopulations
Gnomad4 AFR
AF:
0.277
Gnomad4 AMR
AF:
0.508
Gnomad4 ASJ
AF:
0.509
Gnomad4 EAS
AF:
0.737
Gnomad4 SAS
AF:
0.562
Gnomad4 FIN
AF:
0.593
Gnomad4 NFE
AF:
0.431
Gnomad4 OTH
AF:
0.471
Alfa
AF:
0.427
Hom.:
1788
Bravo
AF:
0.412
Asia WGS
AF:
0.633
AC:
2201
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 26, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
10
DANN
Benign
0.59

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17655355; hg19: chr2-71005101; API