rs533207

Variant names:

• chr11-72137240-A-C
• rs533207
• NM_000804.4:c.168+1120A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000804.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOLR3	NM_000804.4	MANE Select	c.168+1120A>C		intron	N/A	NP_000795.2
	FOLR3	NR_178088.1		n.218+1120A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOLR3	ENST00000611028.3	TSL:1 MANE Select	c.168+1120A>C		intron	N/A	ENSP00000481114.1
	FOLR3	ENST00000612844.4	TSL:1	n.168+1120A>C		intron	N/A	ENSP00000481027.1
	FOLR3	ENST00000622388.4	TSL:5	c.168+1120A>C		intron	N/A	ENSP00000481833.1

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

African (AFR) AF: 0.161 AC: 6571 AN: 40792

American (AMR) AF: 0.0412 AC: 619 AN: 15042

Ashkenazi Jewish (ASJ) AF: 0.0484 AC: 167 AN: 3448

East Asian (EAS) AF: 0.0162 AC: 82 AN: 5070

South Asian (SAS) AF: 0.0168 AC: 80 AN: 4758

European-Finnish (FIN) AF: 0.117 AC: 1200 AN: 10222

Middle Eastern (MID) AF: 0.0207 AC: 6 AN: 290

European-Non Finnish (NFE) AF: 0.0504 AC: 3402 AN: 67508

Other (OTH) AF: 0.0676 AC: 141 AN: 2086

Alfa AF: 0.0811 Hom.: 82

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	-0.97
CADD	Benign	0.41
DANN	Benign	0.73
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs533207; hg19: chr11-71848286;