rs7925055

chr11-72134050-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000622388.4(FOLR3):c.-6-1897A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0813 in 152,222 control chromosomes in the GnomAD database, including 746 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.081 (746 hom., cov: 32)
• Consequence: FOLR3 ENST00000622388.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.06

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOLR3	ENST00000622388.4	c.-6-1897A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0811 AC: 12338 AN: 152104 Hom.: 739 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0439

Gnomad ASJ AF: 0.0482

Gnomad EAS AF: 0.0156

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0501

Gnomad OTH AF: 0.0670

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0813 AC: 12374 AN: 152222 Hom.: 746 Cov.: 32 AF XY: 0.0826 AC XY: 6147 AN XY: 74444

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.0438

Gnomad4 ASJ AF: 0.0482

Gnomad4 EAS AF: 0.0158

Gnomad4 SAS AF: 0.0166

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0501

Gnomad4 OTH AF: 0.0672

Alfa AF: 0.0786 Hom.: 76

Bravo AF: 0.0792

Asia WGS AF: 0.0370 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	11
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7925055; hg19: chr11-71845096;