rs1554819624
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP2
The NM_014000.3(VCL):c.2978G>A(p.Arg993His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,762 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R993C) has been classified as Uncertain significance.
Frequency
Consequence
NM_014000.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VCL | NM_014000.3 | c.2978G>A | p.Arg993His | missense_variant | 20/22 | ENST00000211998.10 | |
VCL | NM_003373.4 | c.2774G>A | p.Arg925His | missense_variant | 19/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VCL | ENST00000211998.10 | c.2978G>A | p.Arg993His | missense_variant | 20/22 | 1 | NM_014000.3 | ||
VCL | ENST00000372755.7 | c.2774G>A | p.Arg925His | missense_variant | 19/21 | 1 | P1 | ||
VCL | ENST00000623461.3 | n.5577G>A | non_coding_transcript_exon_variant | 21/23 | 1 | ||||
VCL | ENST00000624354.3 | c.*2733G>A | 3_prime_UTR_variant, NMD_transcript_variant | 19/21 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152126Hom.: 0 Cov.: 30
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461636Hom.: 0 Cov.: 36 AF XY: 0.00000275 AC XY: 2AN XY: 727114
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152126Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74308
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at