Variant chr11-78109624-T-C 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.899-43A>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 1,536,924 control chromosomes in the GnomAD database, including 26,485 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 4395 hom., cov: 32)

Exomes 𝑓: 0.17 ( 22090 hom. )

Consequence

ALG8
NM_024079.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.261

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:

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=-0.91).

BP6

Variant 11-78109624-T-C is Benign according to our data. Variant chr11-78109624-T-C is described in ClinVar as [Benign]. Clinvar id is 261683.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.899-43A>G		intron_variant		ENST00000299626.10	NP_076984.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALG8	ENST00000299626.10 linkuse as main transcript	c.899-43A>G		intron_variant		1	NM_024079.5	ENSP00000299626	P3	Q9BVK2-1

Frequencies

GnomAD3 genomes

AF:

0.218

AC:

33048

AN:

151832

Hom.:

4392

Cov.:

show subpopulations

Gnomad AFR

AF:

0.379

Gnomad AMI

AF:

0.157

Gnomad AMR

AF:

0.130

Gnomad ASJ

AF:

0.159

Gnomad EAS

AF:

0.284

Gnomad SAS

AF:

0.202

Gnomad FIN

AF:

0.0976

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.158

Gnomad OTH

AF:

0.203

GnomAD3 exomes

AF:

0.181

AC:

43439

AN:

240636

Hom.:

4506

AF XY:

0.180

AC XY:

23497

AN XY:

130372

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:

0.110

Gnomad NFE exome

AF:

0.164

Gnomad OTH exome

AF:

0.174

GnomAD4 exome

AF:

0.172

AC:

237733

AN:

1384976

Hom.:

22090

Cov.:

AF XY:

0.172

AC XY:

118929

AN XY:

693092

show subpopulations

Gnomad4 AFR exome

AF:

0.397

Gnomad4 AMR exome

AF:

0.0980

Gnomad4 ASJ exome

AF:

0.154

Gnomad4 EAS exome

AF:

0.300

Gnomad4 SAS exome

AF:

0.214

Gnomad4 FIN exome

AF:

0.115

Gnomad4 NFE exome

AF:

0.162

Gnomad4 OTH exome

AF:

0.190

GnomAD4 genome

AF:

0.218

AC:

33071

AN:

151948

Hom.:

4395

Cov.:

AF XY:

0.212

AC XY:

15780

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.379

Gnomad4 AMR

AF:

0.130

Gnomad4 ASJ

AF:

0.159

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.:

569

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

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

-0.91

CADD

Benign

2.7

DANN

Benign

0.59

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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