rs752092

chr15-101241729-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014918.5(CHSY1):c.321-6152T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,046 control chromosomes in the GnomAD database, including 15,655 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.

• Frequency: Genomes: 𝑓 0.42 (15655 hom., cov: 32)
• Consequence: CHSY1 NM_014918.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHSY1	NM_014918.5	c.321-6152T>C		intron_variant		ENST00000254190.4
CHSY1	XM_011521364.3	c.321-6152T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHSY1	ENST00000254190.4	c.321-6152T>C		intron_variant		1	NM_014918.5	P1
CHSY1	ENST00000559384.1	n.70+819T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64209 AN: 151928 Hom.: 15622 Cov.: 32

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.431

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.423 AC: 64299 AN: 152046 Hom.: 15655 Cov.: 32 AF XY: 0.418 AC XY: 31041 AN XY: 74336

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.430

Alfa AF: 0.352 Hom.: 20461

Bravo AF: 0.436

Asia WGS AF: 0.238 AC: 825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.98
Dann	Benign	0.37

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

Other links and lift over

dbSNP: rs752092; hg19: chr15-101781934;