1-111241358-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004000.3(CHI3L2):c.950C>T(p.Thr317Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000225 in 1,602,436 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004000.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHI3L2 | NM_004000.3 | c.950C>T | p.Thr317Met | missense_variant | 9/11 | ENST00000369748.9 | |
CHI3L2 | NM_001025197.1 | c.920C>T | p.Thr307Met | missense_variant | 8/10 | ||
CHI3L2 | NM_001025199.2 | c.713C>T | p.Thr238Met | missense_variant | 8/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHI3L2 | ENST00000369748.9 | c.950C>T | p.Thr317Met | missense_variant | 9/11 | 1 | NM_004000.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251438Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135894
GnomAD4 exome AF: 0.0000172 AC: 25AN: 1450284Hom.: 0 Cov.: 27 AF XY: 0.0000111 AC XY: 8AN XY: 722102
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2021 | The c.950C>T (p.T317M) alteration is located in exon 9 (coding exon 9) of the CHI3L2 gene. This alteration results from a C to T substitution at nucleotide position 950, causing the threonine (T) at amino acid position 317 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