11-78102951-CAAAAAA-CAAAAA

Variant names:

• chr11-78102951-CA-C
• rs35218171
• NM_024079.5:c.1349+1028delT

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6 BA1

The NM_001007027.3(ALG8):​c.1350-4delT 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. Variant has been reported in Lovd as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.62 (19500 hom., cov: 0)
  • Exomes 𝑓: 0.39 (21 hom.)
• Consequence: ALG8 NM_001007027.3 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

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 -9 ACMG points.

• BP6: Variant 11-78102951-CA-C is Benign according to our data. Variant chr11-78102951-CA-C is described in Lovd as [Benign]. Variant chr11-78102951-CA-C is described in Lovd as [Benign]. Variant chr11-78102951-CA-C is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALG8	NM_024079.5	c.1349+1028delT		intron_variant	Intron 12 of 12	ENST00000299626.10	NP_076984.2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.618 AC: 73016 AN: 118074 Hom.: 19508 Cov.: 0

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.619

GnomAD3 exomes AF: 0.397 AC: 50 AN: 126 Hom.: 0 AF XY: 0.382 AC XY: 29 AN XY: 76

Gnomad AFR exome AF: 0.500

Gnomad AMR exome AF: 0.382

Gnomad ASJ exome AF: 0.500

Gnomad SAS exome AF: 0.500

Gnomad NFE exome AF: 0.383

Gnomad OTH exome AF: 0.333

GnomAD4 exome AF: 0.388 AC: 629 AN: 1622 Hom.: 21 Cov.: 0 AF XY: 0.388 AC XY: 420 AN XY: 1082

Gnomad4 AFR exome AF: 0.417

Gnomad4 AMR exome AF: 0.367

Gnomad4 ASJ exome AF: 0.417

Gnomad4 EAS exome AF: 0.333

Gnomad4 SAS exome AF: 0.316

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.366

Gnomad4 OTH exome AF: 0.340

GnomAD4 genome AF: 0.618 AC: 73005 AN: 118062 Hom.: 19500 Cov.: 0 AF XY: 0.615 AC XY: 34584 AN XY: 56196

Gnomad4 AFR AF: 0.676

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.620

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs35218171; hg19: chr11-77813997;