Variant chr11-72190626-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000393679.5(FOLR1):c.-24C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0385 in 152,216 control chromosomes in the GnomAD database, including 213 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.038 ( 213 hom., cov: 32)

Exomes 𝑓: 0.043 ( 0 hom. )

Consequence

FOLR1
ENST00000393679.5 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.910

Variant links:

Genes affected

FOLR1 (HGNC:3791): (folate receptor alpha) The protein encoded by this gene is a member of the folate receptor family. Members of this gene family bind folic acid and its reduced derivatives, and transport 5-methyltetrahydrofolate into cells. This gene product is a secreted protein that either anchors to membranes via a glycosyl-phosphatidylinositol linkage or exists in a soluble form. Mutations in this gene have been associated with neurodegeneration due to cerebral folate transport deficiency. Due to the presence of two promoters, multiple transcription start sites, and alternative splicing, multiple transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Oct 2009]

FOLR1 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 11-72190626-C-T is Benign according to our data. Variant chr11-72190626-C-T is described in ClinVar as [Benign]. Clinvar id is 1293890.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	Protein
FOLR1	NM_016724.3 linkuse as main transcript	c.-24C>T	5_prime_UTR_variant	2/6	NP_057936.1
FOLR1	NM_000802.3 linkuse as main transcript	c.-9+695C>T	intron_variant		NP_000793.1
FOLR1	NM_016725.3 linkuse as main transcript	c.-9+867C>T	intron_variant		NP_057937.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000378140.3 linkuse as main transcript	n.419+7887G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0384

AC:

5844

AN:

152050

Hom.:

211

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0928

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0198

Gnomad ASJ

AF:

0.0248

Gnomad EAS

AF:

0.0794

Gnomad SAS

AF:

0.0651

Gnomad FIN

AF:

0.0136

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.00977

Gnomad OTH

AF:

0.0321

GnomAD4 exome

AF:

0.0435

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0625

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0263

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.0385

AC:

5851

AN:

152170

Hom.:

213

Cov.:

AF XY:

0.0395

AC XY:

2942

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.0928

Gnomad4 AMR

AF:

0.0198

Gnomad4 ASJ

AF:

0.0248

Gnomad4 EAS

AF:

0.0794

Gnomad4 SAS

AF:

0.0650

Gnomad4 FIN

AF:

0.0136

Gnomad4 NFE

AF:

0.00979

Gnomad4 OTH

AF:

0.0313

Alfa

AF:

0.0169

Hom.:

Bravo

AF:

0.0412

Asia WGS

AF:

0.0560

AC:

196

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 24, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

5.9

DANN

Benign

0.76

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over