chr1-111230888-A-T
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004000.3(CHI3L2):c.217A>T(p.Ile73Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000403 in 1,614,074 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 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
Publications
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHI3L2 | NM_004000.3 | c.217A>T | p.Ile73Phe | missense_variant | Exon 3 of 11 | ENST00000369748.9 | NP_003991.2 | |
CHI3L2 | NM_001025197.1 | c.187A>T | p.Ile63Phe | missense_variant | Exon 2 of 10 | NP_001020368.1 | ||
CHI3L2 | NM_001025199.2 | c.-21A>T | 5_prime_UTR_variant | Exon 2 of 10 | NP_001020370.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152190Hom.: 0 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.0000119 AC: 3AN: 251410 AF XY: 0.00000736 show subpopulations
GnomAD4 exome AF: 0.0000431 AC: 63AN: 1461884Hom.: 0 Cov.: 32 AF XY: 0.0000413 AC XY: 30AN XY: 727242 show subpopulations
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152190Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74362 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.217A>T (p.I73F) alteration is located in exon 3 (coding exon 3) of the CHI3L2 gene. This alteration results from a A to T substitution at nucleotide position 217, causing the isoleucine (I) at amino acid position 73 to be replaced by a phenylalanine (F). 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