Variant rs190796582 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_080605.4(B3GALT6):c.138C>T(p.Ser46=) 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

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
B3GALT6	NM_080605.4 linkuse as main transcript	c.138C>T	p.Ser46=	synonymous_variant	1/1	ENST00000379198.5	NP_542172.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
B3GALT6	ENST00000379198.5 linkuse as main transcript	c.138C>T	p.Ser46=	synonymous_variant	1/1		NM_080605.4	ENSP00000368496	P1

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

GnomAD3 exomes

AF:

0.0761

AC:

AN:

Hom.:

AF XY:

0.0938

AC XY:

AN XY:

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

Gnomad4 AFR exome

AF:

0.265

Gnomad4 AMR exome

AF:

0.0909

Gnomad4 ASJ exome

AF:

0.0761

Gnomad4 EAS exome

AF:

0.178

Gnomad4 SAS exome

AF:

0.103

Gnomad4 FIN exome

AF:

0.135

Gnomad4 NFE exome

AF:

0.114

Gnomad4 OTH exome

AF:

0.126

GnomAD4 genome

AF:

0.152

AC:

22230

AN:

146274

Hom.:

2075

Cov.:

AF XY:

0.153

AC XY:

10864

AN XY:

71186

show subpopulations

Gnomad4 AFR

AF:

0.262

Gnomad4 AMR

AF:

0.0853

Gnomad4 ASJ

AF:

0.0825

Gnomad4 EAS

AF:

0.173

Gnomad4 SAS

AF:

0.0998

Gnomad4 FIN

AF:

0.117

Gnomad4 NFE

AF:

0.110

Gnomad4 OTH

AF:

0.131

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

Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 29, 2016	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. -
Likely benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Feb 10, 2015	- -

not provided

Benign:1

Likely benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

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

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

5.3

DANN

Benign

0.88

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.6

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