rs202712

chr11-49177372-C-T

Variant summary

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

The NM_004476.3(FOLH1):c.921-1415G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,524 control chromosomes in the GnomAD database, including 11,452 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 0.37 (11452 hom., cov: 31)
• Consequence: FOLH1 NM_004476.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690

Genes affected

FOLH1 (HGNC:3788): (folate hydrolase 1) This gene encodes a type II transmembrane glycoprotein belonging to the M28 peptidase family. The protein acts as a glutamate carboxypeptidase on different alternative substrates, including the nutrient folate and the neuropeptide N-acetyl-l-aspartyl-l-glutamate and is expressed in a number of tissues such as prostate, central and peripheral nervous system and kidney. A mutation in this gene may be associated with impaired intestinal absorption of dietary folates, resulting in low blood folate levels and consequent hyperhomocysteinemia. Expression of this protein in the brain may be involved in a number of pathological conditions associated with glutamate excitotoxicity. In the prostate the protein is up-regulated in cancerous cells and is used as an effective diagnostic and prognostic indicator of prostate cancer. This gene likely arose from a duplication event of a nearby chromosomal region. Alternative splicing gives rise to multiple transcript variants encoding several different isoforms. [provided by RefSeq, Jul 2010]

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 = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FOLH1	NM_004476.3	c.921-1415G>A		intron_variant		ENST00000256999.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOLH1	ENST00000256999.7	c.921-1415G>A		intron_variant		1	NM_004476.3	P1

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55449 AN: 151406 Hom.: 11441 Cov.: 31

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.366 AC: 55497 AN: 151524 Hom.: 11452 Cov.: 31 AF XY: 0.368 AC XY: 27219 AN XY: 74032

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.316

Alfa AF: 0.307 Hom.: 3274

Bravo AF: 0.368

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.6
Dann	Benign	0.35

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: rs202712; hg19: chr11-49198924;