Genetic Variant ALG8:c.1349+1028dupT (chr11-78102951-C-CA) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001007027.3(ALG8):c.1350-4dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.011 ( 42 hom., cov: 0)

Exomes 𝑓: 0.045 ( 0 hom. )

Consequence

ALG8
NM_001007027.3 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.131

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALG8	NM_024079.5 link	c.1349+1028dupT		intron_variant	Intron 12 of 12	ENST00000299626.10	NP_076984.2	Q9BVK2-1A0A024R5K5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALG8	ENST00000299626.10 link	c.1349+1028_1349+1029insT		intron_variant	Intron 12 of 12	1	NM_024079.5	ENSP00000299626.5		Q9BVK2-1

Frequencies

GnomAD3 genomes

AF:

0.0109

AC:

1281

AN:

118000

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00222

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0581

Gnomad ASJ

AF:

0.00628

Gnomad EAS

AF:

0.0808

Gnomad SAS

AF:

0.00579

Gnomad FIN

AF:

0.0116

Gnomad MID

AF:

0.00410

Gnomad NFE

AF:

0.00135

Gnomad OTH

AF:

0.0155

GnomAD3 exomes

AF:

0.0556

AC:

AN:

126

Hom.:

AF XY:

0.0395

AC XY:

AN XY:

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0588

Gnomad ASJ exome

AF:

0.125

Gnomad SAS exome

AF:

0.00

Gnomad NFE exome

AF:

0.0333

Gnomad OTH exome

AF:

0.167

GnomAD4 exome

AF:

0.0451

AC:

AN:

1620

Hom.:

Cov.:

AF XY:

0.0444

AC XY:

AN XY:

1082

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0625

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0741

Gnomad4 SAS exome

AF:

0.0102

Gnomad4 FIN exome

AF:

0.0625

Gnomad4 NFE exome

AF:

0.0632

Gnomad4 OTH exome

AF:

0.0566

GnomAD4 genome

AF:

0.0108

AC:

1274

AN:

117986

Hom.:

Cov.:

AF XY:

0.0123

AC XY:

692

AN XY:

56166

show subpopulations

Gnomad4 AFR

AF:

0.00221

Gnomad4 AMR

AF:

0.0580

Gnomad4 ASJ

AF:

0.00628

Gnomad4 EAS

AF:

0.0799

Gnomad4 SAS

AF:

0.00584

Gnomad4 FIN

AF:

0.0116

Gnomad4 NFE

AF:

0.00135

Gnomad4 OTH

AF:

0.0149

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

11-78102951-CAAAAAA-CAAAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over