Variant chr11-72190447-G-A 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.-203G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0382 in 152,272 control chromosomes in the GnomAD database, including 206 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.038 ( 206 hom., cov: 32)

Exomes 𝑓: 0.042 ( 0 hom. )

Consequence

FOLR1
ENST00000393679.5 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0800

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 11-72190447-G-A is Benign according to our data. Variant chr11-72190447-G-A is described in ClinVar as [Benign]. Clinvar id is 1296043.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
FOLR1	NM_000802.3 linkuse as main transcript	c.-9+516G>A	intron_variant
FOLR1	NM_016724.3 linkuse as main transcript	c.-74-129G>A	intron_variant
FOLR1	NM_016725.3 linkuse as main transcript	c.-9+688G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000378140.3 linkuse as main transcript	n.419+8066C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0382

AC:

5812

AN:

152106

Hom.:

204

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0924

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0197

Gnomad ASJ

AF:

0.0248

Gnomad EAS

AF:

0.0790

Gnomad SAS

AF:

0.0648

Gnomad FIN

AF:

0.0135

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.00960

Gnomad OTH

AF:

0.0312

GnomAD4 exome

AF:

0.0417

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0500

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:

0.0526

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0382

AC:

5819

AN:

152224

Hom.:

206

Cov.:

AF XY:

0.0393

AC XY:

2923

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.0924

Gnomad4 AMR

AF:

0.0197

Gnomad4 ASJ

AF:

0.0248

Gnomad4 EAS

AF:

0.0790

Gnomad4 SAS

AF:

0.0646

Gnomad4 FIN

AF:

0.0135

Gnomad4 NFE

AF:

0.00961

Gnomad4 OTH

AF:

0.0304

Alfa

AF:

0.0172

Hom.:

Bravo

AF:

0.0408

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

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.2

DANN

Benign

0.46

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