Genetic Variant NM_024079.5:c.1349+1028delT (chr11-78102951-CA-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_024079.5(ALG8):c.1349+1028delT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.62 ( 19500 hom., cov: 0)

Exomes 𝑓: 0.39 ( 21 hom. )

Consequence

ALG8
NM_024079.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.131

Publications

0 publications found

Variant links:

Genes affected

ALG8 (HGNC:23161): (ALG8 alpha-1,3-glucosyltransferase) This gene encodes a member of the ALG6/ALG8 glucosyltransferase family. The encoded protein catalyzes the addition of the second glucose residue to the lipid-linked oligosaccharide precursor for N-linked glycosylation of proteins. Mutations in this gene have been associated with congenital disorder of glycosylation type Ih (CDG-Ih). Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ALG8 Gene-Disease associations (from GenCC):

autosomal dominant polycystic kidney disease
Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
ALG8-congenital disorder of glycosylation
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics
polycystic liver disease 3 with or without kidney cysts
Inheritance: AD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Ambry Genetics

ALG8 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024079.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ALG8	NM_024079.5	MANE Select	c.1349+1028delT	intron	N/A	NP_076984.2	A0A024R5K5
ALG8	NM_001425224.1		c.1442+1028delT	intron	N/A	NP_001412153.1
ALG8	NM_001425225.1		c.1397+1028delT	intron	N/A	NP_001412154.1	H0YDD3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ALG8	ENST00000299626.10	TSL:1 MANE Select	c.1349+1028delT	intron	N/A	ENSP00000299626.5	Q9BVK2-1
ALG8	ENST00000679559.1		c.1349+1028delT	intron	N/A	ENSP00000505433.1	A0A7P0T919
ALG8	ENST00000532440.6	TSL:3	c.1397+1028delT	intron	N/A	ENSP00000433429.2	H0YDD3

Frequencies

GnomAD3 genomes

AF:

0.618

AC:

73016

AN:

118074

Hom.:

19508

Cov.:

show subpopulations

Gnomad AFR

AF:

0.676

Gnomad AMI

AF:

0.562

Gnomad AMR

AF:

0.502

Gnomad ASJ

AF:

0.590

Gnomad EAS

AF:

0.579

Gnomad SAS

AF:

0.612

Gnomad FIN

AF:

0.623

Gnomad MID

AF:

0.631

Gnomad NFE

AF:

0.614

Gnomad OTH

AF:

0.619

GnomAD2 exomes

AF:

0.397

AC:

AN:

126

AF XY:

0.382

show subpopulations

Gnomad AFR exome

AF:

0.500

Gnomad AMR exome

AF:

0.382

Gnomad ASJ exome

AF:

0.500

Gnomad NFE exome

AF:

0.383

Gnomad OTH exome

AF:

0.333

GnomAD4 exome

AF:

0.388

AC:

629

AN:

1622

Hom.:

Cov.:

AF XY:

0.388

AC XY:

420

AN XY:

1082

show subpopulations

African (AFR)

AF:

0.417

AC:

AN:

American (AMR)

AF:

0.367

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.417

AC:

AN:

East Asian (EAS)

AF:

0.333

AC:

AN:

South Asian (SAS)

AF:

0.316

AC:

AN:

European-Finnish (FIN)

AF:

0.125

AC:

AN:

Middle Eastern (MID)

AF:

0.494

AC:

175

AN:

354

European-Non Finnish (NFE)

AF:

0.366

AC:

320

AN:

874

Other (OTH)

AF:

0.340

AC:

AN:

106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

118

148

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.618

AC:

73005

AN:

118062

Hom.:

19500

Cov.:

AF XY:

0.615

AC XY:

34584

AN XY:

56196

show subpopulations

African (AFR)

AF:

0.676

AC:

21708

AN:

32104

American (AMR)

AF:

0.502

AC:

5731

AN:

11420

Ashkenazi Jewish (ASJ)

AF:

0.590

AC:

1692

AN:

2868

East Asian (EAS)

AF:

0.580

AC:

2398

AN:

4134

South Asian (SAS)

AF:

0.613

AC:

2205

AN:

3600

European-Finnish (FIN)

AF:

0.623

AC:

3981

AN:

6394

Middle Eastern (MID)

AF:

0.628

AC:

142

AN:

226

European-Non Finnish (NFE)

AF:

0.614

AC:

33757

AN:

55006

Other (OTH)

AF:

0.620

AC:

999

AN:

1612

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1342

2684

4027

5369

6711

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

650

1300

1950

2600

3250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.13

Mutation Taster

=99/1

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over