chrX-111707814-C-T

Position:

• chrX-111707814-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001099922.3(ALG13):​c.384-213C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 111,173 control chromosomes in the GnomAD database, including 7,874 homozygotes. There are 7,390 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.24 (7874 hom., 7390 hem., cov: 23)
• Consequence: ALG13 NM_001099922.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.0330

Genes affected

ALG13 (HGNC:30881): (ALG13 UDP-N-acetylglucosaminyltransferase subunit) The protein encoded by this gene is a subunit of a bipartite UDP-N-acetylglucosamine transferase. It heterodimerizes with asparagine-linked glycosylation 14 homolog to form a functional UDP-GlcNAc glycosyltransferase that catalyzes the second sugar addition of the highly conserved oligosaccharide precursor in endoplasmic reticulum N-linked glycosylation. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2009]

ALG13-AS1 (HGNC:41277): (ALG13 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BP6: Variant X-111707814-C-T is Benign according to our data. Variant chrX-111707814-C-T is described in ClinVar as [Benign]. Clinvar id is 1248507.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 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
ALG13	NM_001099922.3	c.384-213C>T		intron_variant		ENST00000394780.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALG13	ENST00000394780.8	c.384-213C>T		intron_variant		2	NM_001099922.3	A2
ALG13-AS1	ENST00000430794.1	n.107-1077G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.243 AC: 27045 AN: 111118 Hom.: 7868 Cov.: 23 AF XY: 0.220 AC XY: 7341 AN XY: 33346

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.000564

Gnomad SAS AF: 0.00603

Gnomad FIN AF: 0.000495

Gnomad MID AF: 0.0795

Gnomad NFE AF: 0.00687

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.244 AC: 27105 AN: 111173 Hom.: 7874 Cov.: 23 AF XY: 0.221 AC XY: 7390 AN XY: 33411

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0147

Gnomad4 EAS AF: 0.000566

Gnomad4 SAS AF: 0.00529

Gnomad4 FIN AF: 0.000495

Gnomad4 NFE AF: 0.00685

Gnomad4 OTH AF: 0.184

Alfa AF: 0.146 Hom.: 1172

Bravo AF: 0.281

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 26, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	11
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1078540; hg19: chrX-110951042;