1-156700542-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001878.4(CRABP2):c.366G>A(p.Leu122Leu) variant causes a splice region, synonymous change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,248 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L122L) has been classified as Likely benign.
Frequency
Consequence
NM_001878.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CRABP2 | NM_001878.4 | c.366G>A | p.Leu122Leu | splice_region_variant, synonymous_variant | Exon 3 of 4 | ENST00000368222.8 | NP_001869.1 | |
CRABP2 | NM_001199723.2 | c.366G>A | p.Leu122Leu | splice_region_variant, synonymous_variant | Exon 4 of 5 | NP_001186652.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRABP2 | ENST00000368222.8 | c.366G>A | p.Leu122Leu | splice_region_variant, synonymous_variant | Exon 3 of 4 | 1 | NM_001878.4 | ENSP00000357205.3 | ||
CRABP2 | ENST00000368221.1 | c.366G>A | p.Leu122Leu | splice_region_variant, synonymous_variant | Exon 4 of 5 | 3 | ENSP00000357204.1 | |||
CRABP2 | ENST00000621784.4 | c.366G>A | p.Leu122Leu | splice_region_variant, synonymous_variant | Exon 4 of 5 | 3 | ENSP00000482841.1 | |||
ENSG00000285570 | ENST00000650347.1 | n.150-3409C>T | intron_variant | Intron 1 of 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251416Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135874
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460248Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726592
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at