Variant 1-1232289-T-TGCGGCGGGCGTGGCG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP3BP6_Very_StrongBS1BS2

The NM_080605.4(B3GALT6):c.22_36dup(p.Trp8_Ala12dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00213 in 981,116 control chromosomes in the GnomAD database, including 25 homozygotes. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. L4L) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0091 ( 18 hom., cov: 32)

Exomes 𝑓: 0.00092 ( 7 hom. )

Consequence

B3GALT6
NM_080605.4 inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.871

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 -17 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_080605.4

BP6

Variant 1-1232289-T-TGCGGCGGGCGTGGCG is Benign according to our data. Variant chr1-1232289-T-TGCGGCGGGCGTGGCG is described in ClinVar as [Benign]. Clinvar id is 450224.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00911 (1325/145524) while in subpopulation AFR AF= 0.0297 (1206/40652). AF 95% confidence interval is 0.0283. There are 18 homozygotes in gnomad4. There are 625 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 18 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
B3GALT6	NM_080605.4 linkuse as main transcript	c.22_36dup	p.Trp8_Ala12dup	inframe_insertion	1/1	ENST00000379198.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B3GALT6	ENST00000379198.5 linkuse as main transcript	c.22_36dup	p.Trp8_Ala12dup	inframe_insertion	1/1		NM_080605.4	P1

Frequencies

GnomAD3 genomes

AF:

0.00914

AC:

1329

AN:

145418

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0298

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00286

Gnomad ASJ

AF:

0.00354

Gnomad EAS

AF:

0.00461

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00654

Gnomad NFE

AF:

0.000290

Gnomad OTH

AF:

0.00958

GnomAD4 exome

AF:

0.000919

AC:

768

AN:

835592

Hom.:

Cov.:

AF XY:

0.000919

AC XY:

355

AN XY:

386100

show subpopulations

Gnomad4 AFR exome

AF:

0.0336

Gnomad4 AMR exome

AF:

0.00285

Gnomad4 ASJ exome

AF:

0.00597

Gnomad4 EAS exome

AF:

0.00218

Gnomad4 SAS exome

AF:

0.000752

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000159

Gnomad4 OTH exome

AF:

0.00215

GnomAD4 genome

AF:

0.00911

AC:

1325

AN:

145524

Hom.:

Cov.:

AF XY:

0.00882

AC XY:

625

AN XY:

70892

show subpopulations

Gnomad4 AFR

AF:

0.0297

Gnomad4 AMR

AF:

0.00286

Gnomad4 ASJ

AF:

0.00354

Gnomad4 EAS

AF:

0.00462

Gnomad4 SAS

AF:

0.00105

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000290

Gnomad4 OTH

AF:

0.00897

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, flagged submission	clinical testing	GeneDx	Dec 18, 2019	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 17, 2019	- -

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

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 29, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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