rs372003076

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001270764.2(CHST15):​c.1234G>T​(p.Ala412Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A412T) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

CHST15
NM_001270764.2 missense

Scores

4
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.02
Variant links:
Genes affected
CHST15 (HGNC:18137): (carbohydrate sulfotransferase 15) Chondroitin sulfate (CS) is a glycosaminoglycan which is an important structural component of the extracellular matrix and which links to proteins to form proteoglycans. Chondroitin sulfate E (CS-E) is an isomer of chondroitin sulfate in which the C-4 and C-6 hydroxyl groups are sulfated. This gene encodes a type II transmembrane glycoprotein that acts as a sulfotransferase to transfer sulfate to the C-6 hydroxal group of chondroitin sulfate. This gene has also been identified as being co-expressed with RAG1 in B-cells and as potentially acting as a B-cell surface signaling receptor. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2012]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.21700087).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CHST15NM_001270764.2 linkc.1234G>T p.Ala412Ser missense_variant Exon 6 of 8 ENST00000435907.6 NP_001257693.1 Q7LFX5-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CHST15ENST00000435907.6 linkc.1234G>T p.Ala412Ser missense_variant Exon 6 of 8 1 NM_001270764.2 ENSP00000402394.1 Q7LFX5-1
CHST15ENST00000346248.7 linkc.1234G>T p.Ala412Ser missense_variant Exon 6 of 8 1 ENSP00000333947.6 Q7LFX5-1
CHST15ENST00000628426.1 linkc.1234G>T p.Ala412Ser missense_variant Exon 6 of 6 2 ENSP00000485905.1 Q7LFX5-2
CHST15ENST00000476765.1 linkn.149G>T non_coding_transcript_exon_variant Exon 2 of 2 3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
35
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Benign
-0.41
CADD
Uncertain
23
DANN
Uncertain
1.0
DEOGEN2
Benign
0.074
T;T;.
Eigen
Benign
0.18
Eigen_PC
Uncertain
0.24
FATHMM_MKL
Uncertain
0.91
D
LIST_S2
Benign
0.83
T;.;T
M_CAP
Benign
0.024
T
MetaRNN
Benign
0.22
T;T;T
MetaSVM
Benign
-0.91
T
MutationAssessor
Benign
1.8
L;L;L
PrimateAI
Uncertain
0.56
T
PROVEAN
Benign
-1.1
N;N;.
REVEL
Benign
0.11
Sift
Benign
0.33
T;T;.
Sift4G
Benign
0.069
T;T;T
Polyphen
0.69
P;P;P
Vest4
0.40
MutPred
0.53
Gain of disorder (P = 0.0447);Gain of disorder (P = 0.0447);Gain of disorder (P = 0.0447);
MVP
0.49
MPC
0.39
ClinPred
0.92
D
GERP RS
4.7
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.13
gMVP
0.41

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: rs372003076; hg19: chr10-125780885; API