Variant chr9-133255669-CG-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000538324.2(ABO):c.1054del(p.Arg352ValfsTer?) variant causes a frameshift, splice donor 5th base 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. 1/1 splice prediction tools predict no significant impact on normal splicing. 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
ENST00000538324.2 frameshift, splice_donor_5th_base

Scores

Not classified

Clinical Significance

Affects no assertion criteria provided O:1

Conservation

PhyloP100: -1.10

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 made for transcript

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ABO	NM_020469.3 linkuse as main transcript	c.1058del	p.Pro353ArgfsTer23	frameshift_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABO	ENST00000538324.2 linkuse as main transcript	c.1054del	p.Arg352ValfsTer?	frameshift_variant, splice_donor_5th_base_variant	9/9	5		A2

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

GnomAD3 exomes

AF:

0.0561

AC:

11836

AN:

210860

Hom.:

452

AF XY:

0.0564

AC XY:

6525

AN XY:

115784

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 SAS exome

AF:

0.0310

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

Gnomad4 AFR exome

AF:

0.0575

Gnomad4 AMR exome

AF:

0.0295

Gnomad4 ASJ exome

AF:

0.0702

Gnomad4 EAS exome

AF:

0.0000515

Gnomad4 SAS exome

AF:

0.0304

Gnomad4 FIN exome

AF:

0.103

Gnomad4 NFE exome

AF:

0.0688

Gnomad4 OTH exome

AF:

0.0584

GnomAD4 genome

AF:

0.0628

AC:

9551

AN:

152106

Hom.:

367

Cov.:

AF XY:

0.0637

AC XY:

4739

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.0603

Gnomad4 AMR

AF:

0.0423

Gnomad4 ASJ

AF:

0.0664

Gnomad4 EAS

AF:

0.000387

Gnomad4 SAS

AF:

0.0292

Gnomad4 FIN

AF:

0.115

Gnomad4 NFE

AF:

0.0671

Gnomad4 OTH

AF:

0.0582

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

Affects, no assertion criteria provided

literature only

OMIM

Aug 31, 1992

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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