Genetic Variant ABO:c.29-86G>A (chr9-133262254-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000611156.4(ABO):c.29-86G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0942 in 1,184,454 control chromosomes in the GnomAD database, including 7,340 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.10 ( 896 hom., cov: 31)

Exomes 𝑓: 0.093 ( 6444 hom. )

Consequence

ABO
ENST00000611156.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.355

Publications

53 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABO	NR_198898.1 link	n.41-86G>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABO	ENST00000611156.4 link	c.29-86G>A		intron_variant	Intron 1 of 7	5		ENSP00000483265.1		A0A087X0C2

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15303

AN:

152064

Hom.:

893

Cov.:

show subpopulations

Gnomad AFR

AF:

0.107

Gnomad AMI

AF:

0.0802

Gnomad AMR

AF:

0.0707

Gnomad ASJ

AF:

0.134

Gnomad EAS

AF:

0.181

Gnomad SAS

AF:

0.253

Gnomad FIN

AF:

0.137

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0795

Gnomad OTH

AF:

0.0958

GnomAD4 exome

AF:

0.0933

AC:

96297

AN:

1032272

Hom.:

6444

AF XY:

0.100

AC XY:

52661

AN XY:

525058

show subpopulations

African (AFR)

AF:

0.113

AC:

2760

AN:

24518

American (AMR)

AF:

0.0547

AC:

1953

AN:

35700

Ashkenazi Jewish (ASJ)

AF:

0.124

AC:

2819

AN:

22666

East Asian (EAS)

AF:

0.180

AC:

6281

AN:

34890

South Asian (SAS)

AF:

0.260

AC:

18594

AN:

71626

European-Finnish (FIN)

AF:

0.135

AC:

6603

AN:

48838

Middle Eastern (MID)

AF:

0.142

AC:

707

AN:

4964

European-Non Finnish (NFE)

AF:

0.0699

AC:

51940

AN:

742822

Other (OTH)

AF:

0.100

AC:

4640

AN:

46248

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

4330

8659

12989

17318

21648

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1622

3244

4866

6488

8110

<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:

0.101

AC:

15324

AN:

152182

Hom.:

896

Cov.:

AF XY:

0.106

AC XY:

7875

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.107

AC:

4455

AN:

41510

American (AMR)

AF:

0.0708

AC:

1082

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.134

AC:

465

AN:

3468

East Asian (EAS)

AF:

0.181

AC:

937

AN:

5174

South Asian (SAS)

AF:

0.254

AC:

1228

AN:

4826

European-Finnish (FIN)

AF:

0.137

AC:

1451

AN:

10594

Middle Eastern (MID)

AF:

0.0782

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0796

AC:

5410

AN:

68004

Other (OTH)

AF:

0.0948

AC:

200

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

690

1380

2071

2761

3451

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

192

384

576

768

960

<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:

0.0871

Hom.:

1126

Bravo

AF:

0.0898

Asia WGS

AF:

0.194

AC:

675

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.4

(source)

DANN

Benign

0.36

PhyloP100

-0.35

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over