3-143120902-T-A

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_004267.5(CHST2):​c.86T>A​(p.Leu29Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Consequence

CHST2
NM_004267.5 missense

Scores

3
6
10

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.601
Variant links:
Genes affected
CHST2 (HGNC:1970): (carbohydrate sulfotransferase 2) This locus encodes a sulfotransferase protein. The encoded enzyme catalyzes the sulfation of a nonreducing N-acetylglucosamine residue, and may play a role in biosynthesis of 6-sulfosialyl Lewis X antigen. [provided by RefSeq, Aug 2011]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.41914526).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CHST2NM_004267.5 linkc.86T>A p.Leu29Gln missense_variant Exon 2 of 2 ENST00000309575.5 NP_004258.2 Q9Y4C5-1V9HVX9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CHST2ENST00000309575.5 linkc.86T>A p.Leu29Gln missense_variant Exon 2 of 2 1 NM_004267.5 ENSP00000307911.3 Q9Y4C5-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000756

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Jan 01, 2025
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.86T>A (p.L29Q) alteration is located in exon 2 (coding exon 1) of the CHST2 gene. This alteration results from a T to A substitution at nucleotide position 86, causing the leucine (L) at amino acid position 29 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.088
BayesDel_addAF
Uncertain
0.14
D
BayesDel_noAF
Uncertain
-0.040
CADD
Benign
23
DANN
Benign
0.97
DEOGEN2
Benign
0.26
T
Eigen
Uncertain
0.19
Eigen_PC
Benign
0.15
FATHMM_MKL
Benign
0.43
N
LIST_S2
Benign
0.54
T
M_CAP
Pathogenic
0.67
D
MetaRNN
Benign
0.42
T
MetaSVM
Uncertain
0.61
D
MutationAssessor
Benign
0.0
N
PrimateAI
Pathogenic
0.89
D
PROVEAN
Benign
-0.61
N
REVEL
Uncertain
0.48
Sift
Pathogenic
0.0
D
Sift4G
Uncertain
0.051
T
Polyphen
0.98
D
Vest4
0.21
MutPred
0.29
Loss of glycosylation at P34 (P = 0.0075);
MVP
0.97
MPC
1.1
ClinPred
0.54
D
GERP RS
3.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.3
Varity_R
0.35
gMVP
0.27

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs910185506; hg19: chr3-142839744; API