3-143121976-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004267.5(CHST2):āc.1160C>Gā(p.Ala387Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00001 in 1,593,340 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_004267.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHST2 | NM_004267.5 | c.1160C>G | p.Ala387Gly | missense_variant | 2/2 | ENST00000309575.5 | NP_004258.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHST2 | ENST00000309575.5 | c.1160C>G | p.Ala387Gly | missense_variant | 2/2 | 1 | NM_004267.5 | ENSP00000307911 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000128 AC: 3AN: 233568Hom.: 0 AF XY: 0.0000158 AC XY: 2AN XY: 126774
GnomAD4 exome AF: 0.0000104 AC: 15AN: 1441108Hom.: 0 Cov.: 31 AF XY: 0.00000699 AC XY: 5AN XY: 715578
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 13, 2023 | The c.1160C>G (p.A387G) alteration is located in exon 2 (coding exon 1) of the CHST2 gene. This alteration results from a C to G substitution at nucleotide position 1160, causing the alanine (A) at amino acid position 387 to be replaced by a glycine (G). 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