rs137852607
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_003465.3(CHIT1):c.220G>A(p.Glu74Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0044 in 1,613,996 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E74G) has been classified as Uncertain significance.
Frequency
Consequence
NM_003465.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHIT1 | NM_003465.3 | c.220G>A | p.Glu74Lys | missense_variant | 3/11 | ENST00000367229.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHIT1 | ENST00000367229.6 | c.220G>A | p.Glu74Lys | missense_variant | 3/11 | 1 | NM_003465.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00344 AC: 523AN: 152096Hom.: 2 Cov.: 31
GnomAD3 exomes AF: 0.00342 AC: 860AN: 251470Hom.: 1 AF XY: 0.00347 AC XY: 471AN XY: 135906
GnomAD4 exome AF: 0.00450 AC: 6582AN: 1461782Hom.: 24 Cov.: 35 AF XY: 0.00437 AC XY: 3179AN XY: 727188
GnomAD4 genome ? AF: 0.00344 AC: 523AN: 152214Hom.: 2 Cov.: 31 AF XY: 0.00312 AC XY: 232AN XY: 74414
ClinVar
Submissions by phenotype
Chitotriosidase deficiency Uncertain:1Benign:1Other:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 09, 2019 | - - |
Affects, no assertion criteria provided | literature only | OMIM | Sep 01, 2007 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at