11-72140155-G-A

Variant names:

• chr11-72140155-G-A
• rs11235449
• ENST00000897859.1:c.*324G>A

Variant summary

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

The ENST00000897859.1(FOLR3):​c.*324G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,076 control chromosomes in the GnomAD database, including 8,608 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 0.31 (8608 hom., cov: 32)
• Consequence: FOLR3 ENST00000897859.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.399 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.*324G>A		3_prime_UTR	Exon 5 of 5	ENSP00000567918.1

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47152 AN: 151958 Hom.: 8604 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.310 AC: 47183 AN: 152076 Hom.: 8608 Cov.: 32 AF XY: 0.312 AC XY: 23217 AN XY: 74318

African (AFR) AF: 0.120 AC: 4998 AN: 41510

American (AMR) AF: 0.298 AC: 4555 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1724 AN: 3468

East Asian (EAS) AF: 0.204 AC: 1055 AN: 5178

South Asian (SAS) AF: 0.402 AC: 1934 AN: 4810

European-Finnish (FIN) AF: 0.421 AC: 4448 AN: 10556

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27365 AN: 67948

Other (OTH) AF: 0.315 AC: 663 AN: 2108

Alfa AF: 0.335 Hom.: 6702

Bravo AF: 0.289

Asia WGS AF: 0.318 AC: 1111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.52
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs11235449; hg19: chr11-71851199;