Variant 15-101177985-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_014918.5(CHSY1):c.1812G>A(p.Val604=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0154 in 1,614,176 control chromosomes in the GnomAD database, including 335 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.016 ( 31 hom., cov: 33)

Exomes 𝑓: 0.015 ( 304 hom. )

Consequence

CHSY1
NM_014918.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.25

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 -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.43).

BP6

Variant 15-101177985-C-T is Benign according to our data. Variant chr15-101177985-C-T is described in ClinVar as [Benign]. Clinvar id is 466170.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.25 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHSY1	NM_014918.5 linkuse as main transcript	c.1812G>A	p.Val604=	synonymous_variant	3/3	ENST00000254190.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHSY1	ENST00000254190.4 linkuse as main transcript	c.1812G>A	p.Val604=	synonymous_variant	3/3	1	NM_014918.5	P1
CHSY1	ENST00000543813.2 linkuse as main transcript	c.*1127G>A		3_prime_UTR_variant, NMD_transcript_variant	3/3	2

Frequencies

GnomAD3 genomes

AF:

0.0162

AC:

2459

AN:

152196

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00579

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0351

Gnomad ASJ

AF:

0.0256

Gnomad EAS

AF:

0.0690

Gnomad SAS

AF:

0.0166

Gnomad FIN

AF:

0.0264

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0122

Gnomad OTH

AF:

0.0168

GnomAD3 exomes

AF:

0.0242

AC:

6094

AN:

251438

Hom.:

158

AF XY:

0.0224

AC XY:

3044

AN XY:

135910

show subpopulations

Gnomad AFR exome

AF:

0.00406

Gnomad AMR exome

AF:

0.0551

Gnomad ASJ exome

AF:

0.0317

Gnomad EAS exome

AF:

0.0708

Gnomad SAS exome

AF:

0.0121

Gnomad FIN exome

AF:

0.0276

Gnomad NFE exome

AF:

0.0122

Gnomad OTH exome

AF:

0.0235

GnomAD4 exome

AF:

0.0153

AC:

22323

AN:

1461862

Hom.:

304

Cov.:

AF XY:

0.0150

AC XY:

10877

AN XY:

727226

show subpopulations

Gnomad4 AFR exome

AF:

0.00406

Gnomad4 AMR exome

AF:

0.0541

Gnomad4 ASJ exome

AF:

0.0308

Gnomad4 EAS exome

AF:

0.0566

Gnomad4 SAS exome

AF:

0.0123

Gnomad4 FIN exome

AF:

0.0274

Gnomad4 NFE exome

AF:

0.0117

Gnomad4 OTH exome

AF:

0.0182

GnomAD4 genome

AF:

0.0162

AC:

2463

AN:

152314

Hom.:

Cov.:

AF XY:

0.0173

AC XY:

1286

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.00587

Gnomad4 AMR

AF:

0.0352

Gnomad4 ASJ

AF:

0.0256

Gnomad4 EAS

AF:

0.0685

Gnomad4 SAS

AF:

0.0168

Gnomad4 FIN

AF:

0.0264

Gnomad4 NFE

AF:

0.0122

Gnomad4 OTH

AF:

0.0175

Alfa

AF:

0.0154

Hom.:

Bravo

AF:

0.0168

Asia WGS

AF:

0.0360

AC:

123

AN:

3478

EpiCase

AF:

0.0130

EpiControl

AF:

0.0113

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	May 09, 2019	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 16, 2018	- -

Temtamy preaxial brachydactyly syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 29, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

9.2

DANN

Benign

0.85

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