Variant chr11-111783896-CTATAT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_024740.2(ALG9):c.*2496_*2500delATATA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.26 ( 5296 hom., cov: 19)

Failed GnomAD Quality Control

Consequence

ALG9
NM_024740.2 3_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.28

Variant links:

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]

ALG9 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 11-111783896-CTATAT-C is Benign according to our data. Variant chr11-111783896-CTATAT-C is described in ClinVar as [Likely_benign]. Clinvar id is 302379.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALG9	NM_024740.2 link	c.2496_2500delATATA		3_prime_UTR_variant	15/15	ENST00000616540.5	NP_079016.2	Q9H6U8-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALG9	ENST00000616540 link	c.2496_2500delATATA		3_prime_UTR_variant	15/15	1	NM_024740.2	ENSP00000482437.1		Q9H6U8-3
ALG9	ENST00000532425 link	c.2156_2160delATATA		3_prime_UTR_variant	6/6	3		ENSP00000432442.2		H0YCW6

Frequencies

GnomAD3 genomes

AF:

0.262

AC:

38960

AN:

148562

Hom.:

5297

Cov.:

show subpopulations

Gnomad AFR

AF:

0.215

Gnomad AMI

AF:

0.169

Gnomad AMR

AF:

0.341

Gnomad ASJ

AF:

0.343

Gnomad EAS

AF:

0.178

Gnomad SAS

AF:

0.248

Gnomad FIN

AF:

0.242

Gnomad MID

AF:

0.302

Gnomad NFE

AF:

0.279

Gnomad OTH

AF:

0.300

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

GnomAD4 genome

AF:

0.262

AC:

38965

AN:

148666

Hom.:

5296

Cov.:

AF XY:

0.262

AC XY:

18965

AN XY:

72348

show subpopulations

Gnomad4 AFR

AF:

0.215

Gnomad4 AMR

AF:

0.340

Gnomad4 ASJ

AF:

0.343

Gnomad4 EAS

AF:

0.178

Gnomad4 SAS

AF:

0.247

Gnomad4 FIN

AF:

0.242

Gnomad4 NFE

AF:

0.279

Gnomad4 OTH

AF:

0.297

Alfa

AF:

0.252

Hom.:

539

Asia WGS

AF:

0.211

AC:

729

AN:

3450

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Congenital disorder of glycosylation

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over