Variant rs1789032 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_024079.5(ALG8):c.899-46A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 1,525,356 control chromosomes in the GnomAD database, including 26,308 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 4389 hom., cov: 32)

Exomes 𝑓: 0.17 ( 21919 hom. )

Consequence

ALG8
NM_024079.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -3.13

Variant links:

Genes affected

ALG8 (HGNC:23161): (ALG8 alpha-1,3-glucosyltransferase) This gene encodes a member of the ALG6/ALG8 glucosyltransferase family. The encoded protein catalyzes the addition of the second glucose residue to the lipid-linked oligosaccharide precursor for N-linked glycosylation of proteins. Mutations in this gene have been associated with congenital disorder of glycosylation type Ih (CDG-Ih). Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ALG8 links:

ALG8 (HGNC:):

ALG8 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 11-78109627-T-C is Benign according to our data. Variant chr11-78109627-T-C is described in ClinVar as [Benign]. Clinvar id is 261684.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALG8	NM_024079.5 linkuse as main transcript	c.899-46A>G		intron_variant		ENST00000299626.10	NP_076984.2	Q9BVK2-1A0A024R5K5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALG8	ENST00000299626.10 linkuse as main transcript	c.899-46A>G		intron_variant		1	NM_024079.5	ENSP00000299626.5		Q9BVK2-1

Frequencies

GnomAD3 genomes

AF:

0.218

AC:

33031

AN:

151834

Hom.:

4386

Cov.:

show subpopulations

Gnomad AFR

AF:

0.379

Gnomad AMI

AF:

0.157

Gnomad AMR

AF:

0.130

Gnomad ASJ

AF:

0.158

Gnomad EAS

AF:

0.284

Gnomad SAS

AF:

0.201

Gnomad FIN

AF:

0.0976

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.158

Gnomad OTH

AF:

0.203

GnomAD3 exomes

AF:

0.180

AC:

43102

AN:

238798

Hom.:

4469

AF XY:

0.180

AC XY:

23312

AN XY:

129378

show subpopulations

Gnomad AFR exome

AF:

0.389

Gnomad AMR exome

AF:

0.0937

Gnomad ASJ exome

AF:

0.153

Gnomad EAS exome

AF:

0.301

Gnomad SAS exome

AF:

0.219

Gnomad FIN exome

AF:

0.109

Gnomad NFE exome

AF:

0.164

Gnomad OTH exome

AF:

0.174

GnomAD4 exome

AF:

0.171

AC:

235473

AN:

1373408

Hom.:

21919

Cov.:

AF XY:

0.171

AC XY:

117914

AN XY:

687938

show subpopulations

Gnomad4 AFR exome

AF:

0.397

Gnomad4 AMR exome

AF:

0.0979

Gnomad4 ASJ exome

AF:

0.154

Gnomad4 EAS exome

AF:

0.300

Gnomad4 SAS exome

AF:

0.213

Gnomad4 FIN exome

AF:

0.115

Gnomad4 NFE exome

AF:

0.161

Gnomad4 OTH exome

AF:

0.189

GnomAD4 genome

AF:

0.218

AC:

33053

AN:

151948

Hom.:

4389

Cov.:

AF XY:

0.212

AC XY:

15769

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.379

Gnomad4 AMR

AF:

0.130

Gnomad4 ASJ

AF:

0.158

Gnomad4 EAS

AF:

0.284

Gnomad4 SAS

AF:

0.201

Gnomad4 FIN

AF:

0.0976

Gnomad4 NFE

AF:

0.158

Gnomad4 OTH

AF:

0.201

Alfa

AF:

0.187

Hom.:

578

Bravo

AF:

0.229

Asia WGS

AF:

0.226

AC:

786

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 05, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.031

DANN

Benign

0.41

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