Variant 10-72009832-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

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

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.332

Variant links:

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]

CHST3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 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_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHST3	ENST00000373115.5 linkuse as main transcript	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.:

show subpopulations

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.:

Cov.:

AF XY:

0.418

AC XY:

213

AN XY:

510

show subpopulations

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.:

AF XY:

0.341

AC XY:

25320

AN XY:

74320

show subpopulations

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:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Skeletal dysplasia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

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

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