rs4148945

chr10-72009832-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_004273.5(CHST3):c.*1361C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,750 control chromosomes in the GnomAD database, including 10,783 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.35 (10717 hom., cov: 32)
  • Exomes 𝑓: 0.41 (66 hom.)
• Consequence: CHST3 NM_004273.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:4
• Conservation: PhyloP100: -0.332

Genes affected

CHST3 (HGNC:1971): (carbohydrate sulfotransferase 3) This gene encodes an enzyme which catalyzes the sulfation of chondroitin, a proteoglycan found in the extracellular matrix and most cells which is involved in cell migration and differentiation. Mutations in this gene are associated with spondylepiphyseal dysplasia and humerospinal dysostosis. [provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 10-72009832-C-T is Benign according to our data. Variant chr10-72009832-C-T is described in ClinVar as [Benign]. Clinvar id is 300606.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHST3	NM_004273.5	c.*1361C>T		3_prime_UTR_variant	3/3	ENST00000373115.5
CHST3	XM_006718075.5	c.*1361C>T		3_prime_UTR_variant	3/3
CHST3	XM_011540369.3	c.*1361C>T		3_prime_UTR_variant	3/3
CHST3	XM_047426022.1	c.*1361C>T		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHST3	ENST00000373115.5	c.*1361C>T		3_prime_UTR_variant	3/3	1	NM_004273.5	P1

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52475 AN: 151924 Hom.: 10713 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.380

GnomAD4 exome AF: 0.414 AC: 293 AN: 708 Hom.: 66 Cov.: 0 AF XY: 0.418 AC XY: 213 AN XY: 510

Gnomad4 AFR exome AF: 0.0714

Gnomad4 AMR exome AF: 0.375

Gnomad4 ASJ exome AF: 0.417

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.167

Gnomad4 FIN exome AF: 0.402

Gnomad4 NFE exome AF: 0.462

Gnomad4 OTH exome AF: 0.267

GnomAD4 genome AF: 0.345 AC: 52483 AN: 152042 Hom.: 10717 Cov.: 32 AF XY: 0.341 AC XY: 25320 AN XY: 74320

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.374

Alfa AF: 0.434 Hom.: 13828

Bravo AF: 0.332

Asia WGS AF: 0.187 AC: 652 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, single submitter

Submissions by phenotype

Skeletal dysplasia Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Spondyloepiphyseal dysplasia congenita Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Larsen syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Spondyloepiphyseal dysplasia with congenital joint dislocations Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.65
Dann	Benign	0.78
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs4148945; hg19: chr10-73769590; COSMIC: COSV64151065;