chr16-75529562-C-T

Variant summary

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

The NM_024533.5(CHST5):​c.823G>A​(p.Ala275Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,456,858 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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. A275S) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

CHST5
NM_024533.5 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.15
Variant links:
Genes affected
CHST5 (HGNC:1973): (carbohydrate sulfotransferase 5) The protein encoded by this gene belongs to the Gal/GalNAc/GlcNAc 6-O-sulfotransferase (GST) family, members of which catalyze the transfer of sulfate to position 6 of galactose (Gal), N-acetylgalactosamine (GalNAc), or N-acetylglucosamine (GlcNAc) residues within proteoglycans, and sulfation of O-linked sugars of mucin-type acceptors. Carbohydrate sulfation plays a critical role in many biologic processes. This gene is predominantly expressed in colon and small intestine. [provided by RefSeq, Aug 2011]

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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=0.13494277).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CHST5NM_024533.5 linkc.823G>A p.Ala275Thr missense_variant Exon 4 of 4 ENST00000336257.8 NP_078809.2 Q9GZS9-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CHST5ENST00000336257.8 linkc.823G>A p.Ala275Thr missense_variant Exon 4 of 4 1 NM_024533.5 ENSP00000338783.3 Q9GZS9-1
ENSG00000260092ENST00000460606.1 linkn.*922G>A non_coding_transcript_exon_variant Exon 5 of 5 1 ENSP00000457544.1 H3BUA1
ENSG00000260092ENST00000460606.1 linkn.*922G>A 3_prime_UTR_variant Exon 5 of 5 1 ENSP00000457544.1 H3BUA1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000206
AC:
3
AN:
1456858
Hom.:
0
Cov.:
34
AF XY:
0.00000138
AC XY:
1
AN XY:
724860
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000180
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.089
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Benign
-0.41
CADD
Benign
19
DANN
Benign
0.96
DEOGEN2
Benign
0.23
T
Eigen
Benign
-0.52
Eigen_PC
Benign
-0.49
FATHMM_MKL
Benign
0.43
N
LIST_S2
Benign
0.82
T
M_CAP
Uncertain
0.11
D
MetaRNN
Benign
0.13
T
MetaSVM
Benign
-0.83
T
MutationAssessor
Benign
1.5
L
PrimateAI
Uncertain
0.68
T
PROVEAN
Benign
0.060
N
REVEL
Benign
0.13
Sift
Benign
0.33
T
Sift4G
Benign
0.28
T
Polyphen
0.075
B
Vest4
0.071
MutPred
0.42
Gain of phosphorylation at A275 (P = 0.041);
MVP
0.82
MPC
0.59
ClinPred
0.17
T
GERP RS
1.7
Varity_R
0.085
gMVP
0.86

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr16-75563460; API