rs4530793

Variant names:

• chr5-129944120-G-A
• rs4530793
• NM_175856.5:c.1086+35760G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-129944120-G-A
• chr5-129944120-G-C
• chr5-129944120-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_175856.5(CHSY3):​c.1086+35760G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,140 control chromosomes in the GnomAD database, including 7,716 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 0.29 (7716 hom., cov: 33)
• Consequence: CHSY3 NM_175856.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340
• Publications: 3 publications found

Genes affected

CHSY3 (HGNC:24293): (chondroitin sulfate synthase 3) CSS3 is a glycosyltransferase that has both glucuronyltransferase and N-acetylgalactosaminyltransferase activities (Yada et al., 2003 [PubMed 12907687]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHSY3	NM_175856.5	c.1086+35760G>A		intron_variant	Intron 2 of 2	ENST00000305031.5	NP_787052.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHSY3	ENST00000305031.5	c.1086+35760G>A		intron_variant	Intron 2 of 2	1	NM_175856.5	ENSP00000302629.4
CHSY3	ENST00000507545.1	n.274+35760G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43987 AN: 152022 Hom.: 7715 Cov.: 33

Gnomad AFR AF: 0.0858

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.289 AC: 43982 AN: 152140 Hom.: 7716 Cov.: 33 AF XY: 0.285 AC XY: 21163 AN XY: 74360

African (AFR) AF: 0.0856 AC: 3557 AN: 41550

American (AMR) AF: 0.256 AC: 3909 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1293 AN: 3472

East Asian (EAS) AF: 0.233 AC: 1203 AN: 5168

South Asian (SAS) AF: 0.310 AC: 1498 AN: 4826

European-Finnish (FIN) AF: 0.358 AC: 3784 AN: 10568

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27550 AN: 67954

Other (OTH) AF: 0.315 AC: 665 AN: 2114

Alfa AF: 0.363 Hom.: 17808

Bravo AF: 0.271

Asia WGS AF: 0.262 AC: 912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.47
PhyloP100		-0.34
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4530793; hg19: chr5-129279813;