Genetic Variant NM_024079.5: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_024079.5(ALG8):c.1349+1028dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. 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_024079.5 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:

Genome browser will be placed here

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.

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