rs7925545

Variant names:

• chr11-72134495-A-G
• rs7925545
• ENST00000897859.1:c.-6-1452A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000897859.1(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 ENST00000897859.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45
• Publications: 9 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: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000897859.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOLR3	ENST00000897859.1		c.-6-1452A>G		intron	N/A	ENSP00000567918.1
	FOLR3	ENST00000622388.4	TSL:5	c.-6-1452A>G		intron	N/A	ENSP00000481833.1	A0A087WYI3

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

African (AFR) AF: 0.159 AC: 6584 AN: 41536

American (AMR) AF: 0.0409 AC: 626 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0482 AC: 167 AN: 3466

East Asian (EAS) AF: 0.0158 AC: 82 AN: 5194

South Asian (SAS) AF: 0.0168 AC: 81 AN: 4830

European-Finnish (FIN) AF: 0.114 AC: 1206 AN: 10590

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0500 AC: 3404 AN: 68024

Other (OTH) AF: 0.0666 AC: 141 AN: 2116

Alfa AF: 0.0555 Hom.: 1323

Bravo AF: 0.0786

Asia WGS AF: 0.0370 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.3
DANN	Benign	0.47
PhyloP100		1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7925545;

hg19: chr11-71845541;