11-78100748-G-GT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000679559.1(ALG8):c.1452+344_1452+345insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,058 control chromosomes in the GnomAD database, including 3,906 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.21 (3906 hom., cov: 28)
• Consequence: ALG8 ENST00000679559.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.908

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 11-78100748-G-GT is Benign according to our data. Variant chr11-78100748-G-GT is described in ClinVar as [Benign]. Clinvar id is 1235083.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALG8	ENST00000679559.1	c.1452+344_1452+345insA		intron_variant
ALG8	ENST00000680398.1	c.1452+344_1452+345insA		intron_variant

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31678 AN: 151940 Hom.: 3904 Cov.: 28

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.0981

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.202

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.208 AC: 31702 AN: 152058 Hom.: 3906 Cov.: 28 AF XY: 0.204 AC XY: 15143 AN XY: 74334

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.0981

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.200

Alfa AF: 0.0743 Hom.: 83

Bravo AF: 0.216

Asia WGS AF: 0.224 AC: 779 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 05, 2018

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3841745; hg19: chr11-77811794;