Variant 11-72136034-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_000804.4(FOLR3):c.82C>A(p.Arg28=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0516 in 1,613,770 control chromosomes in the GnomAD database, including 2,872 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.080 ( 722 hom., cov: 32)

Exomes 𝑓: 0.049 ( 2150 hom. )

Consequence

FOLR3
NM_000804.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.09

Variant links:

Genes affected

FOLR3 (HGNC:3795): (folate receptor gamma) This gene encodes a member of the folate receptor (FOLR) family of proteins, which have a high affinity for folic acid and for several reduced folic acid derivatives, and mediate delivery of 5-methyltetrahydrofolate to the interior of cells. Expression of this gene may be elevated in ovarian and primary peritoneal carcinoma. This gene is present in a gene cluster on chromosome 11. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

FOLR3 links:

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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=-0.67).

BP6

Variant 11-72136034-C-A is Benign according to our data. Variant chr11-72136034-C-A is described in ClinVar as [Benign]. Clinvar id is 3035466.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-1.09 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FOLR3	NM_000804.4 linkuse as main transcript	c.82C>A	p.Arg28=	synonymous_variant	2/5	ENST00000611028.3	NP_000795.2
FOLR3	NR_178088.1 linkuse as main transcript	n.132C>A		non_coding_transcript_exon_variant	2/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FOLR3	ENST00000611028.3 linkuse as main transcript	c.82C>A	p.Arg28=	synonymous_variant	2/5	1	NM_000804.4	ENSP00000481114	P1	P41439-1
FOLR3	ENST00000612844.4 linkuse as main transcript	c.82C>A	p.Arg28=	synonymous_variant, NMD_transcript_variant	2/5	1		ENSP00000481027		P41439-4
FOLR3	ENST00000622388.4 linkuse as main transcript	c.82C>A	p.Arg28=	synonymous_variant	3/6	5		ENSP00000481833
FOLR3	ENST00000546166.1 linkuse as main transcript	c.76C>A	p.Arg26=	synonymous_variant	1/2	3		ENSP00000446279

Frequencies

GnomAD3 genomes

AF:

0.0803

AC:

12203

AN:

151990

Hom.:

716

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.0407

Gnomad ASJ

AF:

0.0474

Gnomad EAS

AF:

0.0156

Gnomad SAS

AF:

0.0168

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0499

Gnomad OTH

AF:

0.0662

GnomAD3 exomes

AF:

0.0506

AC:

12671

AN:

250280

Hom.:

479

AF XY:

0.0474

AC XY:

6422

AN XY:

135450

show subpopulations

Gnomad AFR exome

AF:

0.160

Gnomad AMR exome

AF:

0.0318

Gnomad ASJ exome

AF:

0.0420

Gnomad EAS exome

AF:

0.0171

Gnomad SAS exome

AF:

0.0177

Gnomad FIN exome

AF:

0.0952

Gnomad NFE exome

AF:

0.0473

Gnomad OTH exome

AF:

0.0554

GnomAD4 exome

AF:

0.0486

AC:

71037

AN:

1461662

Hom.:

2150

Cov.:

AF XY:

0.0474

AC XY:

34446

AN XY:

727120

show subpopulations

Gnomad4 AFR exome

AF:

0.159

Gnomad4 AMR exome

AF:

0.0331

Gnomad4 ASJ exome

AF:

0.0427

Gnomad4 EAS exome

AF:

0.0112

Gnomad4 SAS exome

AF:

0.0174

Gnomad4 FIN exome

AF:

0.0950

Gnomad4 NFE exome

AF:

0.0474

Gnomad4 OTH exome

AF:

0.0530

GnomAD4 genome

AF:

0.0804

AC:

12234

AN:

152108

Hom.:

722

Cov.:

AF XY:

0.0815

AC XY:

6061

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.158

Gnomad4 AMR

AF:

0.0405

Gnomad4 ASJ

AF:

0.0474

Gnomad4 EAS

AF:

0.0158

Gnomad4 SAS

AF:

0.0168

Gnomad4 FIN

AF:

0.113

Gnomad4 NFE

AF:

0.0499

Gnomad4 OTH

AF:

0.0665

Alfa

AF:

0.0535

Hom.:

103

Bravo

AF:

0.0785

Asia WGS

AF:

0.0360

AC:

123

AN:

3478

EpiCase

AF:

0.0438

EpiControl

AF:

0.0392

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

FOLR3-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 12, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

0.34

DANN

Benign

0.80

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over