14-75578850-GTC-G
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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
NM_017791.3 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.105
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]
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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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FLVCR2 | ENST00000238667 | c.-119_-118delCT | 5_prime_UTR_variant | 1/10 | 1 | NM_017791.3 | ENSP00000238667.4 | |||
FLVCR2-AS1 | ENST00000455232.1 | n.737_738delGA | non_coding_transcript_exon_variant | 1/3 | 1 | |||||
FLVCR2-AS1 | ENST00000693551.1 | n.801_802delGA | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.178 AC: 27051AN: 151962Hom.: 2584 Cov.: 28
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GnomAD4 exome AF: 0.167 AC: 124938AN: 749608Hom.: 11026 AF XY: 0.170 AC XY: 66961AN XY: 394224
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GnomAD4 genome AF: 0.178 AC: 27069AN: 152080Hom.: 2581 Cov.: 28 AF XY: 0.178 AC XY: 13216AN XY: 74358
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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 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at