Genetic Variant ABO:p.Pro353ArgfsTer23 (chr9-133255669-CG-C) – ACMG Classification: Benign (-8 pts)

Variant summary

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

The ENST00000611156.4(ABO):c.1058delC(p.Pro353ArgfsTer23) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.064 in 1,597,388 control chromosomes in the GnomAD database, including 3,759 homozygotes. Variant has been reported in ClinVar as Affects (no stars).

Frequency

Genomes: 𝑓 0.063 ( 367 hom., cov: 31)

Exomes 𝑓: 0.064 ( 3392 hom. )

Consequence

ABO
ENST00000611156.4 frameshift

Scores

Not classified

Clinical Significance

Affects no assertion criteria provided O:1

Conservation

PhyloP100: -1.10

Publications

49 publications found

Variant links:

Genes affected

ABO (HGNC:79): (ABO, alpha 1-3-N-acetylgalactosaminyltransferase and alpha 1-3-galactosyltransferase) This gene encodes proteins related to the first discovered blood group system, ABO. Variation in the ABO gene (chromosome 9q34.2) is the basis of the ABO blood group, thus the presence of an allele determines the blood group in an individual. The 'O' blood group is caused by a deletion of guanine-258 near the N-terminus of the protein which results in a frameshift and translation of an almost entirely different protein. Individuals with the A, B, and AB alleles express glycosyltransferase activities that convert the H antigen into the A or B antigen. Other minor alleles have been found for this gene. [provided by RefSeq, Apr 2022]

ABO links:

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ACMG classification

Classification was made for transcript

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

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABO	NR_198898.1 link	n.1072delC		non_coding_transcript_exon_variant	Exon 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABO	ENST00000611156.4 link	c.1058delC	p.Pro353ArgfsTer23	frameshift_variant	Exon 8 of 8	5		ENSP00000483265.1		A0A087X0C2

Frequencies

GnomAD3 genomes

AF:

0.0628

AC:

9545

AN:

151988

Hom.:

367

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0603

Gnomad AMI

AF:

0.121

Gnomad AMR

AF:

0.0424

Gnomad ASJ

AF:

0.0664

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.0292

Gnomad FIN

AF:

0.115

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0671

Gnomad OTH

AF:

0.0589

GnomAD2 exomes

AF:

0.0561

AC:

11836

AN:

210860

AF XY:

0.0564

show subpopulations

Gnomad AFR exome

AF:

0.0647

Gnomad AMR exome

AF:

0.0275

Gnomad ASJ exome

AF:

0.0758

Gnomad EAS exome

AF:

0.000129

Gnomad FIN exome

AF:

0.106

Gnomad NFE exome

AF:

0.0692

Gnomad OTH exome

AF:

0.0601

GnomAD4 exome

AF:

0.0641

AC:

92652

AN:

1445282

Hom.:

3392

Cov.:

AF XY:

0.0628

AC XY:

45095

AN XY:

717730

show subpopulations

African (AFR)

AF:

0.0575

AC:

1901

AN:

33088

American (AMR)

AF:

0.0295

AC:

1224

AN:

41514

Ashkenazi Jewish (ASJ)

AF:

0.0702

AC:

1809

AN:

25778

East Asian (EAS)

AF:

0.0000515

AC:

AN:

38810

South Asian (SAS)

AF:

0.0304

AC:

2567

AN:

84436

European-Finnish (FIN)

AF:

0.103

AC:

5286

AN:

51140

Middle Eastern (MID)

AF:

0.0655

AC:

376

AN:

5738

European-Non Finnish (NFE)

AF:

0.0688

AC:

75995

AN:

1104978

Other (OTH)

AF:

0.0584

AC:

3492

AN:

59800

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

5513

11026

16539

22052

27565

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2796

5592

8388

11184

13980

<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:

0.0628

AC:

9551

AN:

152106

Hom.:

367

Cov.:

AF XY:

0.0637

AC XY:

4739

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.0603

AC:

2499

AN:

41446

American (AMR)

AF:

0.0423

AC:

647

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0664

AC:

230

AN:

3466

East Asian (EAS)

AF:

0.000387

AC:

AN:

5164

South Asian (SAS)

AF:

0.0292

AC:

141

AN:

4826

European-Finnish (FIN)

AF:

0.115

AC:

1222

AN:

10602

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0671

AC:

4564

AN:

67988

Other (OTH)

AF:

0.0582

AC:

123

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

440

881

1321

1762

2202

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

228

342

456

570

<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:

0.0617

Hom.:

Bravo

AF:

0.0574

Asia WGS

AF:

0.0200

AC:

AN:

3478

ClinVar

Significance: Affects

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ABO blood group system

Other:1

Aug 31, 1992

OMIM

Significance:Affects

Review Status:no assertion criteria provided

Collection Method:literature only

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-1.1

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over