rs1198438654
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_014000.3(VCL):c.-4C>T variant causes a 5 prime UTR premature start codon gain change. The variant allele was found at a frequency of 0.00000548 in 1,459,428 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014000.3 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VCL | NM_014000.3 | c.-4C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 22 | ENST00000211998.10 | NP_054706.1 | ||
VCL | NM_014000.3 | c.-4C>T | 5_prime_UTR_variant | Exon 1 of 22 | ENST00000211998.10 | NP_054706.1 | ||
VCL | NM_003373.4 | c.-4C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 21 | NP_003364.1 | |||
VCL | NM_003373.4 | c.-4C>T | 5_prime_UTR_variant | Exon 1 of 21 | NP_003364.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VCL | ENST00000211998 | c.-4C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 22 | 1 | NM_014000.3 | ENSP00000211998.5 | |||
VCL | ENST00000211998 | c.-4C>T | 5_prime_UTR_variant | Exon 1 of 22 | 1 | NM_014000.3 | ENSP00000211998.5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1459428Hom.: 0 Cov.: 31 AF XY: 0.00000551 AC XY: 4AN XY: 725892
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Cardiovascular phenotype Uncertain:1
The c.-4C>T variant is located in the 5' untranslated region (5’UTR) of the VCL gene. This variant results from a C to T substitution 4 nucleotides upstream from the first translated codon. This nucleotide position is highly conserved in available vertebrate species. The evidence for this gene-disease relationship is limited; therefore, the clinical significance of this alteration is unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at