Variant chr11-78114018-A-G 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.674-29T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,555,466 control chromosomes in the GnomAD database, including 26,096 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 4477 hom., cov: 31)

Exomes 𝑓: 0.17 ( 21619 hom. )

Consequence

ALG8
NM_024079.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.264

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=-0.55).

BP6

Variant 11-78114018-A-G is Benign according to our data. Variant chr11-78114018-A-G is described in ClinVar as [Benign]. Clinvar id is 261682.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 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.674-29T>C		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.674-29T>C		intron_variant		1	NM_024079.5	ENSP00000299626.5		Q9BVK2-1

Frequencies

GnomAD3 genomes

AF:

0.218

AC:

33116

AN:

152000

Hom.:

4471

Cov.:

show subpopulations

Gnomad AFR

AF:

0.381

Gnomad AMI

AF:

0.159

Gnomad AMR

AF:

0.130

Gnomad ASJ

AF:

0.159

Gnomad EAS

AF:

0.287

Gnomad SAS

AF:

0.206

Gnomad FIN

AF:

0.0978

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.157

Gnomad OTH

AF:

0.205

GnomAD3 exomes

AF:

0.177

AC:

35128

AN:

197968

Hom.:

3647

AF XY:

0.178

AC XY:

18733

AN XY:

105104

show subpopulations

Gnomad AFR exome

AF:

0.383

Gnomad AMR exome

AF:

0.0963

Gnomad ASJ exome

AF:

0.154

Gnomad EAS exome

AF:

0.295

Gnomad SAS exome

AF:

0.221

Gnomad FIN exome

AF:

0.110

Gnomad NFE exome

AF:

0.159

Gnomad OTH exome

AF:

0.177

GnomAD4 exome

AF:

0.168

AC:

235378

AN:

1403348

Hom.:

21619

Cov.:

AF XY:

0.168

AC XY:

116854

AN XY:

696186

show subpopulations

Gnomad4 AFR exome

AF:

0.393

Gnomad4 AMR exome

AF:

0.0998

Gnomad4 ASJ exome

AF:

0.154

Gnomad4 EAS exome

AF:

0.295

Gnomad4 SAS exome

AF:

0.214

Gnomad4 FIN exome

AF:

0.115

Gnomad4 NFE exome

AF:

0.157

Gnomad4 OTH exome

AF:

0.187

GnomAD4 genome

AF:

0.218

AC:

33143

AN:

152118

Hom.:

4477

Cov.:

AF XY:

0.213

AC XY:

15860

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.381

Gnomad4 AMR

AF:

0.130

Gnomad4 ASJ

AF:

0.159

Gnomad4 EAS

AF:

0.287

Gnomad4 SAS

AF:

0.205

Gnomad4 FIN

AF:

0.0978

Gnomad4 NFE

AF:

0.157

Gnomad4 OTH

AF:

0.202

Alfa

AF:

0.185

Hom.:

603

Bravo

AF:

0.228

Asia WGS

AF:

0.225

AC:

785

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

-0.55

CADD

Benign

DANN

Benign

0.80

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