rs7925055

Variant names:

• chr11-72134050-A-G
• rs7925055
• ENST00000897859.1:c.-6-1897A>G

Variant summary

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

The ENST00000897859.1(FOLR3):​c.-6-1897A>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 ENST00000897859.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.06
• Publications: 6 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.156 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.-6-1897A>G		intron	N/A	ENSP00000567918.1
	FOLR3	ENST00000622388.4	TSL:5	c.-6-1897A>G		intron	N/A	ENSP00000481833.1	A0A087WYI3

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

African (AFR) AF: 0.159 AC: 6602 AN: 41510

American (AMR) AF: 0.0438 AC: 670 AN: 15296

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

East Asian (EAS) AF: 0.0158 AC: 82 AN: 5190

South Asian (SAS) AF: 0.0166 AC: 80 AN: 4824

European-Finnish (FIN) AF: 0.114 AC: 1208 AN: 10594

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

European-Non Finnish (NFE) AF: 0.0501 AC: 3405 AN: 68024

Other (OTH) AF: 0.0672 AC: 142 AN: 2112

Alfa AF: 0.0810 Hom.: 82

Bravo AF: 0.0792

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	-0.87
CADD	Benign	11
DANN	Benign	0.59
PhyloP100		2.1

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: rs7925055;

hg19: chr11-71845096;