11-72139110-CTA-CTATA

Variant names:

• chr11-72139110-C-CTA
• rs71891516
• NM_000804.4:c.320_321dupAT

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_000804.4(FOLR3):​c.320_321dupAT​(p.Glu108MetfsTer24) variant causes a frameshift change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 0)
• Consequence: FOLR3 NM_000804.4 frameshift
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 7.80

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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP6: Variant 11-72139110-C-CTA is Benign according to our data. Variant chr11-72139110-C-CTA is described in ClinVar as [Benign]. Clinvar id is 3035533.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOLR3	NM_000804.4	c.320_321dupAT	p.Glu108MetfsTer24	frameshift_variant	Exon 3 of 5	ENST00000611028.3	NP_000795.2
FOLR3	NR_178088.1	n.498_499dupAT		non_coding_transcript_exon_variant	Exon 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOLR3	ENST00000611028.3	c.320_321dupAT	p.Glu108MetfsTer24	frameshift_variant	Exon 3 of 5	1	NM_000804.4	ENSP00000481114.1
FOLR3	ENST00000612844.4	n.448_449dupAT		non_coding_transcript_exon_variant	Exon 3 of 5	1		ENSP00000481027.1
FOLR3	ENST00000622388.4	c.320_321dupAT	p.Glu108MetfsTer24	frameshift_variant	Exon 4 of 6	5		ENSP00000481833.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD3 exomes AF: 0.0829 AC: 20748 AN: 250286 Hom.: 1167 AF XY: 0.0792 AC XY: 10729 AN XY: 135428

Gnomad AFR exome AF: 0.244

Gnomad AMR exome AF: 0.0518

Gnomad ASJ exome AF: 0.0707

Gnomad EAS exome AF: 0.0754

Gnomad SAS exome AF: 0.0499

Gnomad FIN exome AF: 0.119

Gnomad NFE exome AF: 0.0741

Gnomad OTH exome AF: 0.0855

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

Asia WGS AF: 0.0810 AC: 281 AN: 3478

EpiCase AF: 0.0701

EpiControl AF: 0.0659

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

FOLR3-related disorder Benign:1

Feb 25, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs71891516; hg19: chr11-71850156;