chr14-75634905-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP4_ModerateBP6_ModerateBS1
The NM_017791.3(FLVCR2):c.1021-5C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000934 in 1,606,732 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_017791.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLVCR2 | NM_017791.3 | c.1021-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000238667.9 | |||
FLVCR2 | NM_001195283.2 | c.406-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLVCR2 | ENST00000238667.9 | c.1021-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_017791.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000559 AC: 85AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000152 AC: 38AN: 250204Hom.: 0 AF XY: 0.000148 AC XY: 20AN XY: 135154
GnomAD4 exome AF: 0.0000447 AC: 65AN: 1454588Hom.: 0 Cov.: 29 AF XY: 0.0000414 AC XY: 30AN XY: 724114
GnomAD4 genome AF: 0.000559 AC: 85AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.000471 AC XY: 35AN XY: 74320
ClinVar
Submissions by phenotype
FLVCR2-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 27, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 12, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at