NM_000803.5:c.-24-79T>C

Variant names:

• chr11-72218482-T-C
• rs651646
• NM_000803.5:c.-24-79T>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_000803.5(FOLR2):​c.-24-79T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FOLR2 NM_000803.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 12 publications found

Genes affected

FOLR2 (HGNC:3793): (folate receptor beta) The protein encoded by this gene is a member of the folate receptor (FOLR) family, and these genes exist in a cluster on chromosome 11. Members of this gene family have a high affinity for folic acid and for several reduced folic acid derivatives, and they mediate delivery of 5-methyltetrahydrofolate to the interior of cells. This protein has a 68% and 79% sequence homology with the FOLR1 and FOLR3 proteins, respectively. Although this protein was originally thought to be specific to placenta, it can also exist in other tissues, and it may play a role in the transport of methotrexate in synovial macrophages in rheumatoid arthritis patients. Multiple transcript variants that encode the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000803.5. 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
	FOLR2	NM_000803.5	MANE Select	c.-24-79T>C		intron	N/A	NP_000794.3	P14207
	FOLR2	NM_001113534.2		c.-24-79T>C		intron	N/A	NP_001107006.1	P14207
	FOLR2	NM_001113535.2		c.-12-91T>C		intron	N/A	NP_001107007.1	P14207

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOLR2	ENST00000298223.11	TSL:1 MANE Select	c.-24-79T>C		intron	N/A	ENSP00000298223.6	P14207
	FOLR2	ENST00000868542.1		c.-103T>C		5_prime_UTR_premature_start_codon_gain	Exon 1 of 4	ENSP00000538601.1
	FOLR2	ENST00000868542.1		c.-103T>C		5_prime_UTR	Exon 1 of 4	ENSP00000538601.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1145530 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 574722

African (AFR) AF: 0.00 AC: 0 AN: 26650

American (AMR) AF: 0.00 AC: 0 AN: 34610

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22016

East Asian (EAS) AF: 0.00 AC: 0 AN: 34808

South Asian (SAS) AF: 0.00 AC: 0 AN: 71010

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 46720

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3876

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 856352

Other (OTH) AF: 0.00 AC: 0 AN: 49488

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 916

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.095
DANN	Benign	0.77
PhyloP100		-1.8
PromoterAI		-0.013	Neutral

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: rs651646; hg19: chr11-71929526;