NM_000804.4:c.169-565C>A

Variant names:

• chr11-72138396-C-A
• rs7926875
• NM_000804.4:c.169-565C>A

Variant summary

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

The NM_000804.4(FOLR3):​c.169-565C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0662 in 152,102 control chromosomes in the GnomAD database, including 444 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 (444 hom., cov: 32)
• Consequence: FOLR3 NM_000804.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOLR3	NM_000804.4	c.169-565C>A		intron_variant	Intron 2 of 4	ENST00000611028.3	NP_000795.2
FOLR3	NR_178088.1	n.219-437C>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOLR3	ENST00000611028.3	c.169-565C>A		intron_variant	Intron 2 of 4	1	NM_000804.4	ENSP00000481114.1
FOLR3	ENST00000612844.4	n.169-437C>A		intron_variant	Intron 2 of 4	1		ENSP00000481027.1
FOLR3	ENST00000622388.4	c.169-565C>A		intron_variant	Intron 3 of 5	5		ENSP00000481833.1
FOLR3	ENST00000546166.1	c.163-565C>A		intron_variant	Intron 1 of 1	3		ENSP00000446279.1

Frequencies

GnomAD3 genomes AF: 0.0661 AC: 10048 AN: 151984 Hom.: 443 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0362

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: 0.0498

Gnomad OTH AF: 0.0584

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

GnomAD4 genome AF: 0.0662 AC: 10062 AN: 152102 Hom.: 444 Cov.: 32 AF XY: 0.0677 AC XY: 5036 AN XY: 74350

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.0361

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.0159

Gnomad4 SAS AF: 0.0168

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0498

Gnomad4 OTH AF: 0.0588

Alfa AF: 0.0483 Hom.: 188

Bravo AF: 0.0623

Asia WGS AF: 0.0330 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.64

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: rs7926875; hg19: chr11-71849442;