chr11-72134495-A-G

Variant names:

• chr11-72134495-A-G
• rs7925545
• ENST00000622388.4:c.-6-1452A>G

Variant summary

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

The ENST00000622388.4(FOLR3):​c.-6-1452A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0808 in 152,268 control chromosomes in the GnomAD database, including 738 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 (738 hom., cov: 32)
• Consequence: FOLR3 ENST00000622388.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOLR3	ENST00000622388.4	c.-6-1452A>G		intron_variant	Intron 2 of 5	5		ENSP00000481833.1

Frequencies

GnomAD3 genomes AF: 0.0807 AC: 12275 AN: 152150 Hom.: 731 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0410

Gnomad ASJ AF: 0.0482

Gnomad EAS AF: 0.0156

Gnomad SAS AF: 0.0168

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0500

Gnomad OTH AF: 0.0664

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

GnomAD4 genome AF: 0.0808 AC: 12309 AN: 152268 Hom.: 738 Cov.: 32 AF XY: 0.0820 AC XY: 6102 AN XY: 74444

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.0409

Gnomad4 ASJ AF: 0.0482

Gnomad4 EAS AF: 0.0158

Gnomad4 SAS AF: 0.0168

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0500

Gnomad4 OTH AF: 0.0666

Alfa AF: 0.0507 Hom.: 459

Bravo AF: 0.0786

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	-0.91
CADD	Benign	7.3
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7925545; hg19: chr11-71845541;