chr14-75633770-T-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_017791.3(FLVCR2):c.1020+74T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00101 in 1,180,610 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0047 ( 5 hom., cov: 32)
Exomes 𝑓: 0.00045 ( 4 hom. )
Consequence
FLVCR2
NM_017791.3 intron
NM_017791.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.893
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]
TTLL5 (HGNC:19963): (tubulin tyrosine ligase like 5) This gene encodes a member of the tubulin tyrosine ligase like protein family. This protein interacts with two glucocorticoid receptor coactivators, transcriptional intermediary factor 2 and steroid receptor coactivator 1. This protein may function as a coregulator of glucocorticoid receptor mediated gene induction and repression. This protein may also function as an alpha tubulin polyglutamylase.[provided by RefSeq, Feb 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 14-75633770-T-C is Benign according to our data. Variant chr14-75633770-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1212214.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00473 (720/152296) while in subpopulation AFR AF= 0.0165 (686/41570). AF 95% confidence interval is 0.0155. There are 5 homozygotes in gnomad4. There are 344 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FLVCR2 | NM_017791.3 | c.1020+74T>C | intron_variant | ENST00000238667.9 | NP_060261.2 | |||
FLVCR2 | NM_001195283.2 | c.405+74T>C | intron_variant | NP_001182212.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FLVCR2 | ENST00000238667.9 | c.1020+74T>C | intron_variant | 1 | NM_017791.3 | ENSP00000238667 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00473 AC: 720AN: 152178Hom.: 5 Cov.: 32
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GnomAD4 exome AF: 0.000454 AC: 467AN: 1028314Hom.: 4 AF XY: 0.000367 AC XY: 195AN XY: 531092
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GnomAD4 genome AF: 0.00473 AC: 720AN: 152296Hom.: 5 Cov.: 32 AF XY: 0.00462 AC XY: 344AN XY: 74480
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 17, 2020 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at