Variant rs7176149 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_014918.5(CHSY1):c.303G>C(p.Arg101Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 1,589,722 control chromosomes in the GnomAD database, including 24,785 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.24 ( 5657 hom., cov: 32)

Exomes 𝑓: 0.15 ( 19128 hom. )

Consequence

CHSY1
NM_014918.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 0.0280

Variant links:

Genes affected

CHSY1 (HGNC:17198): (chondroitin sulfate synthase 1) This gene encodes a member of the chondroitin N-acetylgalactosaminyltransferase family. These enzymes possess dual glucuronyltransferase and galactosaminyltransferase activity and play critical roles in the biosynthesis of chondroitin sulfate, a glycosaminoglycan involved in many biological processes including cell proliferation and morphogenesis. Decreased expression of this gene may play a role in colorectal cancer, and mutations in this gene are a cause of temtamy preaxial brachydactyly syndrome. [provided by RefSeq, Dec 2011]

CHSY1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP6

Variant 15-101251154-C-G is Benign according to our data. Variant chr15-101251154-C-G is described in ClinVar as [Benign]. Clinvar id is 585674.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-101251154-C-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.028 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHSY1	NM_014918.5 link	c.303G>C	p.Arg101Arg	synonymous_variant	Exon 1 of 3	ENST00000254190.4	NP_055733.2	Q86X52
CHSY1	XM_011521364.3 link	c.303G>C	p.Arg101Arg	synonymous_variant	Exon 1 of 4		XP_011519666.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHSY1	ENST00000254190.4 link	c.303G>C	p.Arg101Arg	synonymous_variant	Exon 1 of 3	1	NM_014918.5	ENSP00000254190.3		Q86X52

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

35744

AN:

151944

Hom.:

5655

Cov.:

show subpopulations

Gnomad AFR

AF:

0.452

Gnomad AMI

AF:

0.217

Gnomad AMR

AF:

0.219

Gnomad ASJ

AF:

0.129

Gnomad EAS

AF:

0.0748

Gnomad SAS

AF:

0.154

Gnomad FIN

AF:

0.0992

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.151

Gnomad OTH

AF:

0.248

GnomAD3 exomes

AF:

0.151

AC:

31076

AN:

206342

Hom.:

2914

AF XY:

0.148

AC XY:

16817

AN XY:

113880

show subpopulations

Gnomad AFR exome

AF:

0.431

Gnomad AMR exome

AF:

0.161

Gnomad ASJ exome

AF:

0.132

Gnomad EAS exome

AF:

0.0736

Gnomad SAS exome

AF:

0.147

Gnomad FIN exome

AF:

0.0864

Gnomad NFE exome

AF:

0.140

Gnomad OTH exome

AF:

0.159

GnomAD4 exome

AF:

0.154

AC:

220715

AN:

1437660

Hom.:

19128

Cov.:

AF XY:

0.153

AC XY:

108859

AN XY:

713762

show subpopulations

Gnomad4 AFR exome

AF:

0.463

Gnomad4 AMR exome

AF:

0.172

Gnomad4 ASJ exome

AF:

0.138

Gnomad4 EAS exome

AF:

0.0713

Gnomad4 SAS exome

AF:

0.152

Gnomad4 FIN exome

AF:

0.0977

Gnomad4 NFE exome

AF:

0.148

Gnomad4 OTH exome

AF:

0.172

GnomAD4 genome

AF:

0.235

AC:

35782

AN:

152062

Hom.:

5657

Cov.:

AF XY:

0.232

AC XY:

17213

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.451

Gnomad4 AMR

AF:

0.219

Gnomad4 ASJ

AF:

0.129

Gnomad4 EAS

AF:

0.0748

Gnomad4 SAS

AF:

0.155

Gnomad4 FIN

AF:

0.0992

Gnomad4 NFE

AF:

0.151

Gnomad4 OTH

AF:

0.245

Alfa

AF:

0.189

Hom.:

683

Bravo

AF:

0.256

Asia WGS

AF:

0.130

AC:

452

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Aug 10, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 14, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Temtamy preaxial brachydactyly syndrome

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 03, 2025	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 22, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

DANN

Benign

0.73

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over