rs7176149

Variant names:

Variant summary

Our verdict is Benign. The variant received -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

Publications

9 publications found

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 Gene-Disease associations (from GenCC):

temtamy preaxial brachydactyly syndrome
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet

CHSY1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId is 585674.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

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

GnomAD2 exomes

AF:

0.151

AC:

31076

AN:

206342

AF XY:

0.148

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 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

African (AFR)

AF:

0.463

AC:

15200

AN:

32844

American (AMR)

AF:

0.172

AC:

7385

AN:

43048

Ashkenazi Jewish (ASJ)

AF:

0.138

AC:

3555

AN:

25764

East Asian (EAS)

AF:

0.0713

AC:

2778

AN:

38988

South Asian (SAS)

AF:

0.152

AC:

12707

AN:

83544

European-Finnish (FIN)

AF:

0.0977

AC:

4320

AN:

44206

Middle Eastern (MID)

AF:

0.232

AC:

1324

AN:

5708

European-Non Finnish (NFE)

AF:

0.148

AC:

163173

AN:

1103912

Other (OTH)

AF:

0.172

AC:

10273

AN:

59646

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

Heterozygous variant carriers

8708

17416

26124

34832

43540

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5950

11900

17850

23800

29750

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.235

AC:

35782

AN:

152062

Hom.:

5657

Cov.:

AF XY:

0.232

AC XY:

17213

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.451

AC:

18714

AN:

41450

American (AMR)

AF:

0.219

AC:

3347

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.129

AC:

447

AN:

3472

East Asian (EAS)

AF:

0.0748

AC:

386

AN:

5160

South Asian (SAS)

AF:

0.155

AC:

746

AN:

4822

European-Finnish (FIN)

AF:

0.0992

AC:

1050

AN:

10582

Middle Eastern (MID)

AF:

0.282

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.151

AC:

10294

AN:

67964

Other (OTH)

AF:

0.245

AC:

517

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1273

2547

3820

5094

6367

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

350

700

1050

1400

1750

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

Aug 10, 2018

Athena Diagnostics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jun 14, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

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. -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Temtamy preaxial brachydactyly syndrome

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jul 22, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

(source)

DANN

Benign

0.73

PhyloP100

0.028

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over