Variant 14-75578850-GTC-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_017791.3(FLVCR2):c.-119_-118delCT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 901,688 control chromosomes in the GnomAD database, including 13,607 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 2581 hom., cov: 28)

Exomes 𝑓: 0.17 ( 11026 hom. )

Consequence

FLVCR2
NM_017791.3 5_prime_UTR

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 0.105

Variant links:

Genes affected

FLVCR2 (HGNC:20105): (FLVCR choline and putative heme transporter 2) This gene encodes a member of the major facilitator superfamily. The encoded transmembrane protein is a calcium transporter. Unlike the related protein feline leukemia virus subgroup C receptor 1, the protein encoded by this locus does not bind to feline leukemia virus subgroup C envelope protein. The encoded protein may play a role in development of brain vascular endothelial cells, as mutations at this locus have been associated with proliferative vasculopathy and hydranencephaly-hydrocephaly syndrome. Alternatively spliced transcript variants have been described.[provided by RefSeq, Aug 2010]

FLVCR2 links:

FLVCR2-AS1 (HGNC:55854): (FLVCR2 antisense RNA 1)

FLVCR2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 14-75578850-GTC-G is Benign according to our data. Variant chr14-75578850-GTC-G is described in ClinVar as [Benign]. Clinvar id is 314404.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FLVCR2	NM_017791.3 link	c.-119_-118delCT		5_prime_UTR_variant	1/10	ENST00000238667.9	NP_060261.2	Q9UPI3-1
FLVCR2-AS1	NR_110552.1 link	n.737_738delGA		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
FLVCR2	ENST00000238667 link	c.-119_-118delCT	5_prime_UTR_variant	1/10	1	NM_017791.3	ENSP00000238667.4	Q9UPI3-1
FLVCR2-AS1	ENST00000455232.1 link	n.737_738delGA	non_coding_transcript_exon_variant	1/3	1
FLVCR2-AS1	ENST00000693551.1 link	n.801_802delGA	non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.178

AC:

27051

AN:

151962

Hom.:

2584

Cov.:

show subpopulations

Gnomad AFR

AF:

0.218

Gnomad AMI

AF:

0.107

Gnomad AMR

AF:

0.188

Gnomad ASJ

AF:

0.194

Gnomad EAS

AF:

0.0847

Gnomad SAS

AF:

0.223

Gnomad FIN

AF:

0.137

Gnomad MID

AF:

0.217

Gnomad NFE

AF:

0.162

Gnomad OTH

AF:

0.183

GnomAD4 exome

AF:

0.167

AC:

124938

AN:

749608

Hom.:

11026

AF XY:

0.170

AC XY:

66961

AN XY:

394224

show subpopulations

Gnomad4 AFR exome

AF:

0.216

Gnomad4 AMR exome

AF:

0.173

Gnomad4 ASJ exome

AF:

0.196

Gnomad4 EAS exome

AF:

0.0804

Gnomad4 SAS exome

AF:

0.221

Gnomad4 FIN exome

AF:

0.145

Gnomad4 NFE exome

AF:

0.163

Gnomad4 OTH exome

AF:

0.167

GnomAD4 genome

AF:

0.178

AC:

27069

AN:

152080

Hom.:

2581

Cov.:

AF XY:

0.178

AC XY:

13216

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.218

Gnomad4 AMR

AF:

0.188

Gnomad4 ASJ

AF:

0.194

Gnomad4 EAS

AF:

0.0849

Gnomad4 SAS

AF:

0.222

Gnomad4 FIN

AF:

0.137

Gnomad4 NFE

AF:

0.162

Gnomad4 OTH

AF:

0.184

Alfa

AF:

0.165

Hom.:

276

Bravo

AF:

0.178

Asia WGS

AF:

0.177

AC:

619

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 26, 2021

- -

Fowler syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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