11-78100680-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000679559.1(ALG8):c.1452+413A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 152,198 control chromosomes in the GnomAD database, including 34,918 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.67 (34918 hom., cov: 34)
• Consequence: ALG8 ENST00000679559.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.827

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 11-78100680-T-C is Benign according to our data. Variant chr11-78100680-T-C is described in ClinVar as [Benign]. Clinvar id is 1224993.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.826 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+413A>G		intron_variant
ALG8	ENST00000680398.1	c.1452+413A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101623 AN: 152080 Hom.: 34877 Cov.: 34

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.668 AC: 101715 AN: 152198 Hom.: 34918 Cov.: 34 AF XY: 0.665 AC XY: 49461 AN XY: 74408

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.649

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.652

Alfa AF: 0.626 Hom.: 5102

Bravo AF: 0.668

Asia WGS AF: 0.658 AC: 2293 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

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.48
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2845556; hg19: chr11-77811726;