22-22244961-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007128.4(VPREB1):c.62C>T(p.Pro21Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,614,122 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007128.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VPREB1 | NM_007128.4 | c.62C>T | p.Pro21Leu | missense_variant | Exon 2 of 2 | ENST00000403807.4 | NP_009059.1 | |
VPREB1 | NM_001303509.2 | c.59C>T | p.Pro20Leu | missense_variant, splice_region_variant | Exon 2 of 2 | NP_001290438.1 | ||
IGL | n.22244961C>T | intragenic_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VPREB1 | ENST00000403807.4 | c.62C>T | p.Pro21Leu | missense_variant | Exon 2 of 2 | 1 | NM_007128.4 | ENSP00000385361.3 | ||
VPREB1 | ENST00000302273.2 | c.59C>T | p.Pro20Leu | missense_variant, splice_region_variant | Exon 2 of 2 | 3 | ENSP00000304590.3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 251008Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135678
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461874Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727238
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.62C>T (p.P21L) alteration is located in exon 2 (coding exon 2) of the VPREB1 gene. This alteration results from a C to T substitution at nucleotide position 62, causing the proline (P) at amino acid position 21 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at