chr1-203225058-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_003465.3(CHIT1):c.304G>A(p.Gly102Ser) variant causes a missense change. The variant allele was found at a frequency of 0.301 in 1,611,948 control chromosomes in the GnomAD database, including 73,780 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_003465.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.297 AC: 45014AN: 151466Hom.: 6716 Cov.: 30
GnomAD3 exomes AF: 0.305 AC: 76573AN: 251020Hom.: 11856 AF XY: 0.301 AC XY: 40782AN XY: 135684
GnomAD4 exome AF: 0.301 AC: 440170AN: 1460362Hom.: 67051 Cov.: 34 AF XY: 0.300 AC XY: 218266AN XY: 726572
GnomAD4 genome AF: 0.297 AC: 45064AN: 151586Hom.: 6729 Cov.: 30 AF XY: 0.298 AC XY: 22062AN XY: 74026
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2Other:1
- -
Variant interpreted as Benign and reported on 11-13-2019 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. -
- -
This variant is associated with the following publications: (PMID: 24060732, 19725875, 17000706) -
Chitotriosidase deficiency Benign:2Other:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
- -
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at