13-37000344-CAA-C

Position:

• chr13-37000344-CAA-C

Variant summary

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

The ENST00000681893.1(ALG5):​c.-34+351_-34+352delTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0188 in 100,342 control chromosomes in the GnomAD database, including 21 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.017 (21 hom., cov: 0)
  • Exomes 𝑓: 0.16 (0 hom.)
• Consequence: ALG5 ENST00000681893.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.208

Genes affected

ALG5 (HGNC:20266): (ALG5 dolichyl-phosphate beta-glucosyltransferase) This gene encodes a member of the glycosyltransferase 2 family. The encoded protein participates in glucosylation of the oligomannose core in N-linked glycosylation of proteins. The addition of glucose residues to the oligomannose core is necessary to ensure substrate recognition, and therefore, effectual transfer of the oligomannose core to the nascent glycoproteins. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 13-37000344-CAA-C is Benign according to our data. Variant chr13-37000344-CAA-C is described in ClinVar as [Benign]. Clinvar id is 1275077.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.37000345_37000346delAA		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALG5	ENST00000681893.1	c.-34+351_-34+352delTT		intron_variant				ENSP00000506235.1
EXOSC8	ENST00000489088.5	n.379+1151_379+1152delAA		intron_variant		3
ALG5	ENST00000680949.1	n.-34+351_-34+352delTT		intron_variant				ENSP00000506156.1

Frequencies

GnomAD3 genomes AF: 0.0167 AC: 1652 AN: 98892 Hom.: 21 Cov.: 0

Gnomad AFR AF: 0.0532

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00750

Gnomad ASJ AF: 0.000811

Gnomad EAS AF: 0.00305

Gnomad SAS AF: 0.00112

Gnomad FIN AF: 0.00798

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00117

Gnomad OTH AF: 0.00627

GnomAD4 exome AF: 0.160 AC: 235 AN: 1472 Hom.: 0 AF XY: 0.155 AC XY: 149 AN XY: 960

Gnomad4 AFR exome AF: 0.269

Gnomad4 AMR exome AF: 0.211

Gnomad4 ASJ exome AF: 0.167

Gnomad4 EAS exome AF: 0.167

Gnomad4 SAS exome AF: 0.159

Gnomad4 FIN exome AF: 0.100

Gnomad4 NFE exome AF: 0.152

Gnomad4 OTH exome AF: 0.111

GnomAD4 genome AF: 0.0167 AC: 1655 AN: 98870 Hom.: 21 Cov.: 0 AF XY: 0.0165 AC XY: 776 AN XY: 46892

Gnomad4 AFR AF: 0.0532

Gnomad4 AMR AF: 0.00750

Gnomad4 ASJ AF: 0.000811

Gnomad4 EAS AF: 0.00306

Gnomad4 SAS AF: 0.00114

Gnomad4 FIN AF: 0.00798

Gnomad4 NFE AF: 0.00117

Gnomad4 OTH AF: 0.00626

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

May 20, 2021

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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: rs5802852; hg19: chr13-37574481;