1-111229743-G-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001025199.2(CHI3L2):c.-306G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0129 in 1,412,358 control chromosomes in the GnomAD database, including 1,165 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001025199.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHI3L2 | NM_004000.3 | c.41-109G>T | intron_variant | ENST00000369748.9 | NP_003991.2 | |||
CHI3L2 | NM_001025199.2 | c.-306G>T | 5_prime_UTR_premature_start_codon_gain_variant | 1/10 | NP_001020370.1 | |||
CHI3L2 | NM_001025199.2 | c.-306G>T | 5_prime_UTR_variant | 1/10 | NP_001020370.1 | |||
CHI3L2 | NM_001025197.1 | c.41-999G>T | intron_variant | NP_001020368.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHI3L2 | ENST00000369748.9 | c.41-109G>T | intron_variant | 1 | NM_004000.3 | ENSP00000358763.4 |
Frequencies
GnomAD3 genomes AF: 0.0535 AC: 7667AN: 143434Hom.: 616 Cov.: 29
GnomAD4 exome AF: 0.00830 AC: 10531AN: 1268854Hom.: 543 Cov.: 32 AF XY: 0.00816 AC XY: 5113AN XY: 626730
GnomAD4 genome AF: 0.0537 AC: 7701AN: 143504Hom.: 622 Cov.: 29 AF XY: 0.0530 AC XY: 3683AN XY: 69532
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at