dbSNP rs3826107: CHST5:p.Thr318Met (chr16-75529432-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024533.5(CHST5):c.953C>T(p.Thr318Met) variant causes a missense change. The variant allele was found at a frequency of 0.183 in 1,612,534 control chromosomes in the GnomAD database, including 28,588 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.17 ( 2330 hom., cov: 33)

Exomes 𝑓: 0.18 ( 26258 hom. )

Consequence

CHST5
NM_024533.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.32

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]

CHST5 links:

ENSG00000260092 (HGNC:):

ENSG00000260092 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0019461811).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHST5	NM_024533.5 link	c.953C>T	p.Thr318Met	missense_variant	Exon 4 of 4	ENST00000336257.8	NP_078809.2	Q9GZS9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
CHST5	ENST00000336257.8 link	c.953C>T	p.Thr318Met	missense_variant	Exon 4 of 4	1	NM_024533.5	ENSP00000338783.3	Q9GZS9-1
ENSG00000260092	ENST00000460606.1 link	n.*1052C>T		non_coding_transcript_exon_variant	Exon 5 of 5	1		ENSP00000457544.1	H3BUA1
ENSG00000260092	ENST00000460606.1 link	n.*1052C>T		3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000457544.1	H3BUA1

Frequencies

GnomAD3 genomes

AF:

0.170

AC:

25806

AN:

152120

Hom.:

2328

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.289

Gnomad AMR

AF:

0.144

Gnomad ASJ

AF:

0.0960

Gnomad EAS

AF:

0.201

Gnomad SAS

AF:

0.0888

Gnomad FIN

AF:

0.218

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.202

Gnomad OTH

AF:

0.162

GnomAD3 exomes

AF:

0.163

AC:

40433

AN:

248110

Hom.:

3729

AF XY:

0.164

AC XY:

22068

AN XY:

134652

show subpopulations

Gnomad AFR exome

AF:

0.119

Gnomad AMR exome

AF:

0.0962

Gnomad ASJ exome

AF:

0.0924

Gnomad EAS exome

AF:

0.176

Gnomad SAS exome

AF:

0.0898

Gnomad FIN exome

AF:

0.214

Gnomad NFE exome

AF:

0.204

Gnomad OTH exome

AF:

0.179

GnomAD4 exome

AF:

0.185

AC:

270075

AN:

1460296

Hom.:

26258

Cov.:

AF XY:

0.183

AC XY:

132922

AN XY:

726504

show subpopulations

Gnomad4 AFR exome

AF:

0.115

Gnomad4 AMR exome

AF:

0.101

Gnomad4 ASJ exome

AF:

0.0965

Gnomad4 EAS exome

AF:

0.189

Gnomad4 SAS exome

AF:

0.0913

Gnomad4 FIN exome

AF:

0.216

Gnomad4 NFE exome

AF:

0.199

Gnomad4 OTH exome

AF:

0.172

GnomAD4 genome

AF:

0.170

AC:

25819

AN:

152238

Hom.:

2330

Cov.:

AF XY:

0.168

AC XY:

12493

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.122

Gnomad4 AMR

AF:

0.144

Gnomad4 ASJ

AF:

0.0960

Gnomad4 EAS

AF:

0.201

Gnomad4 SAS

AF:

0.0889

Gnomad4 FIN

AF:

0.218

Gnomad4 NFE

AF:

0.202

Gnomad4 OTH

AF:

0.164

Alfa

AF:

0.181

Hom.:

2642

Bravo

AF:

0.162

TwinsUK

AF:

0.201

AC:

747

ALSPAC

AF:

0.196

AC:

756

ESP6500AA

AF:

0.122

AC:

537

ESP6500EA

AF:

0.198

AC:

1701

ExAC

AF:

0.166

AC:

20161

Asia WGS

AF:

0.176

AC:

608

AN:

3478

EpiCase

AF:

0.196

EpiControl

AF:

0.203

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.43

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.65

Eigen

Uncertain

0.40

Eigen_PC

Uncertain

0.23

FATHMM_MKL

Uncertain

0.97

LIST_S2

Benign

0.81

MetaRNN

Benign

0.0019

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.9

PrimateAI

Uncertain

0.67

PROVEAN

Uncertain

-2.5

REVEL

Benign

0.17

Sift

Uncertain

0.025

Sift4G

Benign

0.078

Polyphen

1.0

Vest4

0.18

MPC

1.5

ClinPred

0.025

GERP RS

2.8

Varity_R

0.34

gMVP

0.80

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over