11-72137240-A-C

Position:

• chr11-72137240-A-C

Variant summary

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

The NM_000804.4(FOLR3):​c.168+1120A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0818 in 150,122 control chromosomes in the GnomAD database, including 734 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 0.082 (734 hom., cov: 31)
• Consequence: FOLR3 NM_000804.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

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]

FOLR3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FOLR3	NM_000804.4	c.168+1120A>C		intron_variant		ENST00000611028.3	NP_000795.2
FOLR3	NR_178088.1	n.218+1120A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FOLR3	ENST00000611028.3	c.168+1120A>C		intron_variant		1	NM_000804.4	ENSP00000481114.1
FOLR3	ENST00000612844.4	n.168+1120A>C		intron_variant		1		ENSP00000481027.1
FOLR3	ENST00000622388.4	c.168+1120A>C		intron_variant		5		ENSP00000481833.1
FOLR3	ENST00000546166.1	c.162+1120A>C		intron_variant		3		ENSP00000446279.1

Frequencies

GnomAD3 genomes AF: 0.0816 AC: 12246 AN: 150008 Hom.: 727 Cov.: 31

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0413

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.0159

Gnomad SAS AF: 0.0168

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0256

Gnomad NFE AF: 0.0504

Gnomad OTH AF: 0.0673

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

GnomAD4 genome AF: 0.0818 AC: 12280 AN: 150122 Hom.: 734 Cov.: 31 AF XY: 0.0831 AC XY: 6083 AN XY: 73180

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.0412

Gnomad4 ASJ AF: 0.0484

Gnomad4 EAS AF: 0.0162

Gnomad4 SAS AF: 0.0168

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0504

Gnomad4 OTH AF: 0.0676

Alfa AF: 0.0785 Hom.: 76

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	-0.97
CADD	Benign	0.41
DANN	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs533207; hg19: chr11-71848286;