11-111825716-T-C

Variant names:

• chr11-111825716-T-C
• rs610437
• NM_024740.2:c.1602+10449A>G

Variant summary

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

The NM_024740.2(ALG9):​c.1602+10449A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 152,006 control chromosomes in the GnomAD database, including 31,024 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.64 (31024 hom., cov: 31)
• Consequence: ALG9 NM_024740.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.765

Genes affected

ALG9 (HGNC:15672): (ALG9 alpha-1,2-mannosyltransferase) This gene encodes an alpha-1,2-mannosyltransferase enzyme that functions in lipid-linked oligosaccharide assembly. Mutations in this gene result in congenital disorder of glycosylation type Il. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

ENSG00000258529 (HGNC:):

ALG9-IT1 (HGNC:41409): (ALG9 intronic transcript 1)

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 11-111825716-T-C is Benign according to our data. Variant chr11-111825716-T-C is described in ClinVar as [Benign]. Clinvar id is 1166805.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALG9	NM_024740.2	c.1602+10449A>G		intron_variant	Intron 13 of 14	ENST00000616540.5	NP_079016.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALG9	ENST00000616540.5	c.1602+10449A>G		intron_variant	Intron 13 of 14	1	NM_024740.2	ENSP00000482437.1
ENSG00000258529	ENST00000622211.4	c.2280+10449A>G		intron_variant	Intron 17 of 18	2		ENSP00000482396.1

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96951 AN: 151888 Hom.: 31015 Cov.: 31

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.638 AC: 97005 AN: 152006 Hom.: 31024 Cov.: 31 AF XY: 0.643 AC XY: 47781 AN XY: 74284

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.640

Alfa AF: 0.625 Hom.: 3535

Bravo AF: 0.642

Asia WGS AF: 0.668 AC: 2325 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

ALG9 congenital disorder of glycosylation Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.34

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: rs610437; hg19: chr11-111696440;