rs8043243

Positions:

• chr15-101231248-C-T

Variant summary

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

The NM_014918.5(CHSY1):​c.816+3834G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 152,088 control chromosomes in the GnomAD database, including 15,333 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 0.43 (15333 hom., cov: 32)
• Consequence: CHSY1 NM_014918.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHSY1	NM_014918.5	c.816+3834G>A		intron_variant		ENST00000254190.4	NP_055733.2
CHSY1	XM_011521364.3	c.816+3834G>A		intron_variant			XP_011519666.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHSY1	ENST00000254190.4	c.816+3834G>A		intron_variant		1	NM_014918.5	ENSP00000254190	P1
CHSY1	ENST00000543813.2	c.66+3834G>A		intron_variant, NMD_transcript_variant		2		ENSP00000496160

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64740 AN: 151970 Hom.: 15309 Cov.: 32

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.0335

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.426 AC: 64808 AN: 152088 Hom.: 15333 Cov.: 32 AF XY: 0.421 AC XY: 31324 AN XY: 74344

Gnomad4 AFR AF: 0.635

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.0335

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.425

Alfa AF: 0.390 Hom.: 6622

Bravo AF: 0.430

Asia WGS AF: 0.192 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.4
DANN	Benign	0.65

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: rs8043243; hg19: chr15-101771453;