11-72139110-C-CTA

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Likely_benign. The variant received -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 VariationId is 3035533.Status of the report is criteria_provided_single_submitter, 1 stars.

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_321dupAT	p.Glu108MetfsTer24	frameshift	Exon 3 of 5	NP_000795.2	P41439-1
	FOLR3	NR_178088.1		n.498_499dupAT		non_coding_transcript_exon	Exon 3 of 5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOLR3	ENST00000611028.3	TSL:1 MANE Select	c.320_321dupAT	p.Glu108MetfsTer24	frameshift	Exon 3 of 5	ENSP00000481114.1	P41439-1
	FOLR3	ENST00000612844.4	TSL:1	n.448_449dupAT		non_coding_transcript_exon	Exon 3 of 5	ENSP00000481027.1	P41439-4
	FOLR3	ENST00000897859.1		c.320_321dupAT	p.Glu108MetfsTer24	frameshift	Exon 3 of 5	ENSP00000567918.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD2 exomes AF: 0.0829 AC: 20748 AN: 250286 AF XY: 0.0792

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 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

Alfa AF: 0.0512 Hom.: 5677

Asia WGS AF: 0.0810 AC: 281 AN: 3478

EpiCase AF: 0.0701

EpiControl AF: 0.0659

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	FOLR3-related disorder (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

Other links and lift over

dbSNP: rs71891516; hg19: chr11-71850156; COSMIC: COSV61529842; COSMIC: COSV61529842;