dbSNP rs71891516: FOLR3:p.Tyr107fs (chr11-72139110-CTA-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_000804.4(FOLR3):c.320_321delAT(p.Tyr107fs) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.918 in 1,613,676 control chromosomes in the GnomAD database, including 681,325 homozygotes. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.87 ( 58449 hom., cov: 0)

Exomes 𝑓: 0.92 ( 622876 hom. )

Consequence

FOLR3
NM_000804.4 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 7.80

Publications

5 publications found

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 was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 11-72139110-CTA-C is Benign according to our data. Variant chr11-72139110-CTA-C is described in ClinVar as Benign. ClinVar VariationId is 768461.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000804.4. 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
	FOLR3	NM_000804.4	MANE Select	c.320_321delAT	p.Tyr107fs	frameshift	Exon 3 of 5	NP_000795.2	P41439-1
	FOLR3	NR_178088.1		n.498_499delAT		non_coding_transcript_exon	Exon 3 of 5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FOLR3	ENST00000611028.3	TSL:1 MANE Select	c.320_321delAT	p.Tyr107fs	frameshift	Exon 3 of 5	ENSP00000481114.1	P41439-1
FOLR3	ENST00000612844.4	TSL:1	n.448_449delAT		non_coding_transcript_exon	Exon 3 of 5	ENSP00000481027.1	P41439-4
FOLR3	ENST00000897859.1		c.320_321delAT	p.Tyr107fs	frameshift	Exon 3 of 5	ENSP00000567918.1

Frequencies

GnomAD3 genomes

AF:

0.873

AC:

132711

AN:

151980

Hom.:

58426

Cov.:

show subpopulations

Gnomad AFR

AF:

0.749

Gnomad AMI

AF:

0.970

Gnomad AMR

AF:

0.928

Gnomad ASJ

AF:

0.924

Gnomad EAS

AF:

0.924

Gnomad SAS

AF:

0.951

Gnomad FIN

AF:

0.861

Gnomad MID

AF:

0.937

Gnomad NFE

AF:

0.924

Gnomad OTH

AF:

0.902

GnomAD4 exome

AF:

0.923

AC:

1348482

AN:

1461578

Hom.:

622876

AF XY:

0.924

AC XY:

671815

AN XY:

727058

show subpopulations

African (AFR)

AF:

0.746

AC:

24985

AN:

33478

American (AMR)

AF:

0.945

AC:

42271

AN:

44710

Ashkenazi Jewish (ASJ)

AF:

0.932

AC:

24332

AN:

26120

East Asian (EAS)

AF:

0.926

AC:

36780

AN:

39698

South Asian (SAS)

AF:

0.951

AC:

81988

AN:

86250

European-Finnish (FIN)

AF:

0.882

AC:

47098

AN:

53400

Middle Eastern (MID)

AF:

0.944

AC:

5445

AN:

5768

European-Non Finnish (NFE)

AF:

0.927

AC:

1030376

AN:

1111784

Other (OTH)

AF:

0.914

AC:

55207

AN:

60370

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

6274

12548

18822

25096

31370

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21538

43076

64614

86152

107690

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.873

AC:

132773

AN:

152098

Hom.:

58449

Cov.:

AF XY:

0.873

AC XY:

64910

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.748

AC:

31019

AN:

41462

American (AMR)

AF:

0.928

AC:

14200

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.924

AC:

3206

AN:

3468

East Asian (EAS)

AF:

0.924

AC:

4777

AN:

5170

South Asian (SAS)

AF:

0.951

AC:

4594

AN:

4832

European-Finnish (FIN)

AF:

0.861

AC:

9103

AN:

10570

Middle Eastern (MID)

AF:

0.946

AC:

278

AN:

294

European-Non Finnish (NFE)

AF:

0.924

AC:

62812

AN:

67986

Other (OTH)

AF:

0.902

AC:

1901

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

846

1692

2538

3384

4230

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

894

1788

2682

3576

4470

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.371

Hom.:

5677

Bravo

AF:

0.873

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

7.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over