chr15-101177901-G-A

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.1896C>T(p.Val632Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0167 in 1,614,172 control chromosomes in the GnomAD database, including 454 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.018 ( 39 hom., cov: 33)

Exomes 𝑓: 0.016 ( 415 hom. )

Consequence

CHSY1
NM_014918.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.0910

Publications

5 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=-0.76).

BP6

Variant 15-101177901-G-A is Benign according to our data. Variant chr15-101177901-G-A is described in ClinVar as Benign. ClinVar VariationId is 466171.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.091 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0901 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014918.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHSY1	NM_014918.5	MANE Select	c.1896C>T	p.Val632Val	synonymous	Exon 3 of 3	NP_055733.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
CHSY1	ENST00000254190.4	TSL:1 MANE Select	c.1896C>T	p.Val632Val	synonymous	Exon 3 of 3	ENSP00000254190.3
CHSY1	ENST00000543813.2	TSL:2	n.*1211C>T		non_coding_transcript_exon	Exon 3 of 3	ENSP00000496160.1
CHSY1	ENST00000543813.2	TSL:2	n.*1211C>T		3_prime_UTR	Exon 3 of 3	ENSP00000496160.1

Frequencies

GnomAD3 genomes

AF:

0.0183

AC:

2786

AN:

152186

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00890

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0358

Gnomad ASJ

AF:

0.0256

Gnomad EAS

AF:

0.0975

Gnomad SAS

AF:

0.0174

Gnomad FIN

AF:

0.0265

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0126

Gnomad OTH

AF:

0.0225

GnomAD2 exomes

AF:

0.0270

AC:

6788

AN:

251478

AF XY:

0.0249

show subpopulations

Gnomad AFR exome

AF:

0.00714

Gnomad AMR exome

AF:

0.0555

Gnomad ASJ exome

AF:

0.0317

Gnomad EAS exome

AF:

0.101

Gnomad FIN exome

AF:

0.0276

Gnomad NFE exome

AF:

0.0124

Gnomad OTH exome

AF:

0.0257

GnomAD4 exome

AF:

0.0165

AC:

24095

AN:

1461868

Hom.:

415

Cov.:

AF XY:

0.0161

AC XY:

11741

AN XY:

727230

show subpopulations

African (AFR)

AF:

0.00681

AC:

228

AN:

33480

American (AMR)

AF:

0.0543

AC:

2430

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.0308

AC:

805

AN:

26134

East Asian (EAS)

AF:

0.0843

AC:

3346

AN:

39700

South Asian (SAS)

AF:

0.0135

AC:

1166

AN:

86258

European-Finnish (FIN)

AF:

0.0274

AC:

1463

AN:

53420

Middle Eastern (MID)

AF:

0.0127

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.0119

AC:

13264

AN:

1111990

Other (OTH)

AF:

0.0219

AC:

1320

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

1528

3057

4585

6114

7642

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

578

1156

1734

2312

2890

<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:

0.0183

AC:

2792

AN:

152304

Hom.:

Cov.:

AF XY:

0.0193

AC XY:

1441

AN XY:

74488

show subpopulations

African (AFR)

AF:

0.00900

AC:

374

AN:

41562

American (AMR)

AF:

0.0359

AC:

549

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.0256

AC:

AN:

3470

East Asian (EAS)

AF:

0.0971

AC:

503

AN:

5180

South Asian (SAS)

AF:

0.0176

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.0265

AC:

281

AN:

10614

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0126

AC:

855

AN:

68026

Other (OTH)

AF:

0.0237

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

151

301

452

602

753

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

144

180

<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:

0.0132

Hom.:

Bravo

AF:

0.0192

Asia WGS

AF:

0.0510

AC:

177

AN:

3478

EpiCase

AF:

0.0135

EpiControl

AF:

0.0116

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

May 08, 2019

Athena Diagnostics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Oct 16, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Temtamy preaxial brachydactyly syndrome

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

1.0

(source)

DANN

Benign

0.69

PhyloP100

-0.091

Mutation Taster

=99/1

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over