chr1-111230840-T-C
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_004000.3(CHI3L2):c.169T>C(p.Ser57Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,614,010 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts 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
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHI3L2 | NM_004000.3 | c.169T>C | p.Ser57Pro | missense_variant | Exon 3 of 11 | ENST00000369748.9 | NP_003991.2 | |
CHI3L2 | NM_001025197.1 | c.139T>C | p.Ser47Pro | missense_variant | Exon 2 of 10 | NP_001020368.1 | ||
CHI3L2 | NM_001025199.2 | c.-69T>C | 5_prime_UTR_variant | Exon 2 of 10 | NP_001020370.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152052Hom.: 0 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.0000318 AC: 8AN: 251458 AF XY: 0.0000221 show subpopulations
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461840Hom.: 1 Cov.: 32 AF XY: 0.00000825 AC XY: 6AN XY: 727228 show subpopulations
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152170Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74386 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.169T>C (p.S57P) alteration is located in exon 3 (coding exon 3) of the CHI3L2 gene. This alteration results from a T to C substitution at nucleotide position 169, causing the serine (S) at amino acid position 57 to be replaced by a proline (P). 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