chr1-156700069-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001878.4(CRABP2):c.374C>T(p.Thr125Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,613,446 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_001878.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRABP2 | ENST00000368222.8 | c.374C>T | p.Thr125Met | missense_variant | Exon 4 of 4 | 1 | NM_001878.4 | ENSP00000357205.3 | ||
CRABP2 | ENST00000368221.1 | c.374C>T | p.Thr125Met | missense_variant | Exon 5 of 5 | 3 | ENSP00000357204.1 | |||
CRABP2 | ENST00000621784.4 | c.374C>T | p.Thr125Met | missense_variant | Exon 5 of 5 | 3 | ENSP00000482841.1 | |||
ENSG00000285570 | ENST00000650347.1 | n.150-3882G>A | intron_variant | Intron 1 of 1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249424Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134896
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461280Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726870
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.374C>T (p.T125M) alteration is located in exon 4 (coding exon 4) of the CRABP2 gene. This alteration results from a C to T substitution at nucleotide position 374, causing the threonine (T) at amino acid position 125 to be replaced by a methionine (M). 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