Genetic Variant FLVCR2:p.Ser40_Ile41insValHisProSerValSerValHisProSerValSerValHisProSerValSer (chr14-75579044-C-CCCCAGCGTCTCGGTCCATCCCAGCGTCTCGGTCCATCCCAGCGTCTCGGTCCAT) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM4

The NM_017791.3(FLVCR2):c.119_120insGGTCCATCCCAGCGTCTCGGTCCATCCCAGCGTCTCGGTCCATCCCAGCGTCTC(p.Ser40_Ile41insValHisProSerValSerValHisProSerValSerValHisProSerValSer) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,310 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

FLVCR2
NM_017791.3 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.380

Publications

0 publications found

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 was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_017791.3.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017791.3. 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
	FLVCR2	NM_017791.3	MANE Select	c.119_120insGGTCCATCCCAGCGTCTCGGTCCATCCCAGCGTCTCGGTCCATCCCAGCGTCTC	p.Ser40_Ile41insValHisProSerValSerValHisProSerValSerValHisProSerValSer	disruptive_inframe_insertion	Exon 1 of 10	NP_060261.2	Q9UPI3-1
	FLVCR2-AS1	NR_110552.1		n.544_545insATGGACCGAGACGCTGGGATGGACCGAGACGCTGGGATGGACCGAGACGCTGGG		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FLVCR2	ENST00000238667.9	TSL:1 MANE Select	c.119_120insGGTCCATCCCAGCGTCTCGGTCCATCCCAGCGTCTCGGTCCATCCCAGCGTCTC	p.Ser40_Ile41insValHisProSerValSerValHisProSerValSerValHisProSerValSer	disruptive_inframe_insertion	Exon 1 of 10	ENSP00000238667.4	Q9UPI3-1
FLVCR2-AS1	ENST00000455232.2	TSL:1	n.544_545insATGGACCGAGACGCTGGGATGGACCGAGACGCTGGGATGGACCGAGACGCTGGG		non_coding_transcript_exon	Exon 1 of 3
FLVCR2	ENST00000852195.1		c.119_120insGGTCCATCCCAGCGTCTCGGTCCATCCCAGCGTCTCGGTCCATCCCAGCGTCTC	p.Ser40_Ile41insValHisProSerValSerValHisProSerValSerValHisProSerValSer	disruptive_inframe_insertion	Exon 1 of 11	ENSP00000522253.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

6.84e-7

AC:

AN:

1461310

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

726972

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33440

American (AMR)

AF:

0.00

AC:

AN:

44716

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26134

East Asian (EAS)

AF:

0.00

AC:

AN:

39682

South Asian (SAS)

AF:

0.00

AC:

AN:

86222

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53412

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

9.00e-7

AC:

AN:

1111570

Other (OTH)

AF:

0.00

AC:

AN:

60366

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

14-75579044-CCCCAGCGTCTCGGTCCAT-CCCCAGCGTCTCGGTCCATCCCAGCGTCTCGGTCCATCCCAGCGTCTCGGTCCATCCCAGCGTCTCGGTCCAT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over