rs190796582

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_080605.4(B3GALT6):c.138C>T(p.Ser46Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 990,228 control chromosomes in the GnomAD database, including 8,160 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 2075 hom., cov: 33)

Exomes 𝑓: 0.12 ( 6085 hom. )

Consequence

B3GALT6
NM_080605.4 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.620

Publications

7 publications found

Variant links:

Genes affected

B3GALT6 (HGNC:17978): (beta-1,3-galactosyltransferase 6) The enzyme encoded by this intronless gene is a beta-1,3-galactosyltransferase found in the medial Golgi apparatus, where it catalyzes the transfer of galactose from UDP-galactose to substrates containing a terminal beta-linked galactose moiety. The encoded enzyme has a particular affinity for galactose-beta-1,4-xylose found in the linker region of glycosamines. This enzyme is required for glycosaminoglycan synthesis. [provided by RefSeq, Jun 2013]

B3GALT6 Gene-Disease associations (from GenCC):

Ehlers-Danlos syndrome, spondylodysplastic type, 2
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P, Genomics England PanelApp
spondyloepimetaphyseal dysplasia with joint laxity, type 1, with or without fractures
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
spondyloepimetaphyseal dysplasia with joint laxity
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

B3GALT6 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP6

Variant 1-1232416-C-T is Benign according to our data. Variant chr1-1232416-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 193478.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.62 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B3GALT6	NM_080605.4 link	c.138C>T	p.Ser46Ser	synonymous_variant	Exon 1 of 1	ENST00000379198.5	NP_542172.2	Q96L58

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GALT6	ENST00000379198.5 link	c.138C>T	p.Ser46Ser	synonymous_variant	Exon 1 of 1	6	NM_080605.4	ENSP00000368496.2		Q96L58

Frequencies

GnomAD3 genomes

AF:

0.152

AC:

22172

AN:

146168

Hom.:

2050

Cov.:

show subpopulations

Gnomad AFR

AF:

0.261

Gnomad AMI

AF:

0.0998

Gnomad AMR

AF:

0.0857

Gnomad ASJ

AF:

0.0825

Gnomad EAS

AF:

0.172

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.117

Gnomad MID

AF:

0.106

Gnomad NFE

AF:

0.110

Gnomad OTH

AF:

0.133

GnomAD2 exomes

AF:

0.0761

AC:

AN:

AF XY:

0.0938

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.125

Gnomad ASJ exome

AF:

0.00

Gnomad NFE exome

AF:

0.0857

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.117

AC:

98855

AN:

843954

Hom.:

6085

Cov.:

AF XY:

0.117

AC XY:

45720

AN XY:

391040

show subpopulations

African (AFR)

AF:

0.265

AC:

4231

AN:

15956

American (AMR)

AF:

0.0909

AC:

122

AN:

1342

Ashkenazi Jewish (ASJ)

AF:

0.0761

AC:

408

AN:

5362

East Asian (EAS)

AF:

0.178

AC:

711

AN:

3984

South Asian (SAS)

AF:

0.103

AC:

1790

AN:

17372

European-Finnish (FIN)

AF:

0.135

AC:

183

AN:

1356

Middle Eastern (MID)

AF:

0.0938

AC:

155

AN:

1652

European-Non Finnish (NFE)

AF:

0.114

AC:

87722

AN:

768994

Other (OTH)

AF:

0.126

AC:

3533

AN:

27936

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

5836

11672

17508

23344

29180

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.152

AC:

22230

AN:

146274

Hom.:

2075

Cov.:

AF XY:

0.153

AC XY:

10864

AN XY:

71186

show subpopulations

African (AFR)

AF:

0.262

AC:

10705

AN:

40846

American (AMR)

AF:

0.0853

AC:

1257

AN:

14730

Ashkenazi Jewish (ASJ)

AF:

0.0825

AC:

279

AN:

3382

East Asian (EAS)

AF:

0.173

AC:

877

AN:

5080

South Asian (SAS)

AF:

0.0998

AC:

479

AN:

4800

European-Finnish (FIN)

AF:

0.117

AC:

980

AN:

8380

Middle Eastern (MID)

AF:

0.103

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.110

AC:

7264

AN:

65814

Other (OTH)

AF:

0.131

AC:

268

AN:

2040

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

927

1853

2780

3706

4633

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.138

Hom.:

211

Asia WGS

AF:

0.130

AC:

269

AN:

2074

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Feb 10, 2015

Eurofins Ntd Llc (ga)

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Sep 29, 2016

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Spondyloepimetaphyseal dysplasia with joint laxity;C3809210:Ehlers-Danlos syndrome, spondylodysplastic type, 2

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

5.3

(source)

DANN

Benign

0.88

PhyloP100

-0.62

PromoterAI

-0.0083

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.6

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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rs190796582

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over