Variant rs4148943 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.*1278C>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 0.435 in 152,322 control chromosomes in the GnomAD database, including 14,753 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.44 ( 14723 hom., cov: 33)

Exomes 𝑓: 0.43 ( 30 hom. )

Consequence

CHST3
NM_004273.5 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.109

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=-0.65).

BP6

Variant 10-72009749-C-T is Benign according to our data. Variant chr10-72009749-C-T is described in ClinVar as [Benign]. Clinvar id is 300604.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
CHST3	NM_004273.5 linkuse as main transcript	c.*1278C>T	3_prime_UTR_variant	3/3	ENST00000373115.5	NP_004264.2
CHST3	XM_006718075.5 linkuse as main transcript	c.*1278C>T	3_prime_UTR_variant	3/3		XP_006718138.1
CHST3	XM_011540369.3 linkuse as main transcript	c.*1278C>T	3_prime_UTR_variant	3/3		XP_011538671.1
CHST3	XM_047426022.1 linkuse as main transcript	c.*1278C>T	3_prime_UTR_variant	3/3		XP_047281978.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHST3	ENST00000373115.5 linkuse as main transcript	c.*1278C>T		3_prime_UTR_variant	3/3	1	NM_004273.5	ENSP00000362207	P1

Frequencies

GnomAD3 genomes

AF:

0.435

AC:

66145

AN:

151914

Hom.:

14709

Cov.:

show subpopulations

Gnomad AFR

AF:

0.430

Gnomad AMI

AF:

0.432

Gnomad AMR

AF:

0.414

Gnomad ASJ

AF:

0.418

Gnomad EAS

AF:

0.124

Gnomad SAS

AF:

0.303

Gnomad FIN

AF:

0.429

Gnomad MID

AF:

0.439

Gnomad NFE

AF:

0.478

Gnomad OTH

AF:

0.450

GnomAD4 exome

AF:

0.434

AC:

126

AN:

290

Hom.:

Cov.:

AF XY:

0.409

AC XY:

AN XY:

132

show subpopulations

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.250

Gnomad4 FIN exome

AF:

0.416

Gnomad4 NFE exome

AF:

0.484

Gnomad4 OTH exome

AF:

0.667

GnomAD4 genome

AF:

0.435

AC:

66190

AN:

152032

Hom.:

14723

Cov.:

AF XY:

0.427

AC XY:

31734

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.430

Gnomad4 AMR

AF:

0.414

Gnomad4 ASJ

AF:

0.418

Gnomad4 EAS

AF:

0.124

Gnomad4 SAS

AF:

0.303

Gnomad4 FIN

AF:

0.429

Gnomad4 NFE

AF:

0.478

Gnomad4 OTH

AF:

0.444

Alfa

AF:

0.468

Hom.:

22940

Bravo

AF:

0.434

Asia WGS

AF:

0.221

AC:

772

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

-0.65

CADD

Benign

9.4

DANN

Benign

0.87

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