13-37000344-CA-C

Position:

• chr13-37000344-CA-C

Variant summary

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

The ENST00000681893.1(ALG5):​c.-34+352del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.82 (32686 hom., cov: 0)
  • Exomes 𝑓: 0.39 (9 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]

EXOSC8 (HGNC:17035): (exosome component 8) This gene encodes a 3'-5' exoribonuclease that specifically interacts with mRNAs containing AU-rich elements. The encoded protein is part of the exosome complex that is important for the degradation of numerous RNA species. A pseudogene of this gene is found on chromosome 6. [provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 13-37000344-CA-C is Benign according to our data. Variant chr13-37000344-CA-C is described in ClinVar as [Benign]. Clinvar id is 1295035.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALG5	ENST00000681893.1	c.-34+352del		intron_variant				ENSP00000506235
ALG5	ENST00000680949.1	c.-34+352del		intron_variant, NMD_transcript_variant				ENSP00000506156
EXOSC8	ENST00000489088.5	n.379+1169del		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.823 AC: 81428 AN: 98960 Hom.: 32709 Cov.: 0

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.913

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.840

GnomAD4 exome AF: 0.392 AC: 582 AN: 1484 Hom.: 9 Cov.: 0 AF XY: 0.397 AC XY: 384 AN XY: 968

Gnomad4 AFR exome AF: 0.464

Gnomad4 AMR exome AF: 0.422

Gnomad4 ASJ exome AF: 0.417

Gnomad4 EAS exome AF: 0.533

Gnomad4 SAS exome AF: 0.395

Gnomad4 FIN exome AF: 0.400

Gnomad4 NFE exome AF: 0.371

Gnomad4 OTH exome AF: 0.444

GnomAD4 genome AF: 0.823 AC: 81392 AN: 98938 Hom.: 32686 Cov.: 0 AF XY: 0.825 AC XY: 38727 AN XY: 46934

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.842

Gnomad4 EAS AF: 0.954

Gnomad4 SAS AF: 0.906

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.805

Gnomad4 OTH AF: 0.840

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

Jun 03, 2021

- -

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;