11-72138457-C-G

Variant names:

• chr11-72138457-C-G
• rs7926987
• NM_000804.4:c.169-504C>G

Variant summary

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

The NM_000804.4(FOLR3):​c.169-504C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0663 in 152,220 control chromosomes in the GnomAD database, including 448 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 0.066 (448 hom., cov: 32)
• Consequence: FOLR3 NM_000804.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOLR3	NM_000804.4	MANE Select	c.169-504C>G		intron	N/A	NP_000795.2	P41439-1
	FOLR3	NR_178088.1		n.219-376C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOLR3	ENST00000611028.3	TSL:1 MANE Select	c.169-504C>G		intron	N/A	ENSP00000481114.1	P41439-1
	FOLR3	ENST00000612844.4	TSL:1	n.169-376C>G		intron	N/A	ENSP00000481027.1	P41439-4
	FOLR3	ENST00000897860.1		c.169-376C>G		intron	N/A	ENSP00000567919.1

Frequencies

GnomAD3 genomes AF: 0.0662 AC: 10070 AN: 152102 Hom.: 447 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0361

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.0156

Gnomad SAS AF: 0.0168

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0499

Gnomad OTH AF: 0.0584

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

GnomAD4 genome AF: 0.0663 AC: 10085 AN: 152220 Hom.: 448 Cov.: 32 AF XY: 0.0679 AC XY: 5050 AN XY: 74418

African (AFR) AF: 0.107 AC: 4463 AN: 41532

American (AMR) AF: 0.0360 AC: 551 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0481 AC: 167 AN: 3472

East Asian (EAS) AF: 0.0158 AC: 82 AN: 5184

South Asian (SAS) AF: 0.0168 AC: 81 AN: 4820

European-Finnish (FIN) AF: 0.114 AC: 1207 AN: 10586

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0499 AC: 3393 AN: 68016

Other (OTH) AF: 0.0588 AC: 124 AN: 2110

Alfa AF: 0.0292 Hom.: 23

Bravo AF: 0.0623

Asia WGS AF: 0.0330 AC: 114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.16
DANN	Benign	0.39
PhyloP100		-2.2
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: rs7926987; hg19: chr11-71849503;