dbSNP rs8176717: ABO:c.240-105C>A (chr9-133257647-G-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.240-105C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 1,391,948 control chromosomes in the GnomAD database, including 42,320 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 0.26 ( 5392 hom., cov: 32)

Exomes 𝑓: 0.24 ( 36928 hom. )

Consequence

ABO
ENST00000611156.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.21

Publications

18 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=-0.88).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABO	NR_198898.1 link	n.252-105C>A		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABO	ENST00000611156.4 link	c.240-105C>A		intron_variant	Intron 5 of 7	5		ENSP00000483265.1

Frequencies

GnomAD3 genomes

AF:

0.258

AC:

39149

AN:

151800

Hom.:

5387

Cov.:

show subpopulations

Gnomad AFR

AF:

0.269

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.380

Gnomad ASJ

AF:

0.276

Gnomad EAS

AF:

0.269

Gnomad SAS

AF:

0.213

Gnomad FIN

AF:

0.178

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.240

Gnomad OTH

AF:

0.248

GnomAD4 exome

AF:

0.239

AC:

296211

AN:

1240030

Hom.:

36928

AF XY:

0.236

AC XY:

144663

AN XY:

612464

show subpopulations

African (AFR)

AF:

0.261

AC:

7405

AN:

28350

American (AMR)

AF:

0.454

AC:

14798

AN:

32614

Ashkenazi Jewish (ASJ)

AF:

0.272

AC:

5883

AN:

21640

East Asian (EAS)

AF:

0.258

AC:

8977

AN:

34760

South Asian (SAS)

AF:

0.199

AC:

13900

AN:

69866

European-Finnish (FIN)

AF:

0.174

AC:

6337

AN:

36392

Middle Eastern (MID)

AF:

0.218

AC:

799

AN:

3668

European-Non Finnish (NFE)

AF:

0.234

AC:

225048

AN:

960454

Other (OTH)

AF:

0.250

AC:

13064

AN:

52286

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

9624

19249

28873

38498

48122

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7728

15456

23184

30912

38640

<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:

0.258

AC:

39169

AN:

151918

Hom.:

5392

Cov.:

AF XY:

0.257

AC XY:

19114

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.268

AC:

11087

AN:

41318

American (AMR)

AF:

0.381

AC:

5820

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.276

AC:

958

AN:

3468

East Asian (EAS)

AF:

0.269

AC:

1385

AN:

5156

South Asian (SAS)

AF:

0.213

AC:

1025

AN:

4816

European-Finnish (FIN)

AF:

0.178

AC:

1890

AN:

10590

Middle Eastern (MID)

AF:

0.252

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.240

AC:

16319

AN:

67978

Other (OTH)

AF:

0.246

AC:

519

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1460

2920

4379

5839

7299

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

390

780

1170

1560

1950

<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:

0.260

Hom.:

8533

Bravo

AF:

0.278

Asia WGS

AF:

0.263

AC:

914

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.29

(source)

DANN

Benign

0.62

PhyloP100

-1.2

RBP_binding_hub_radar

1.0

RBP_regulation_power_radar

3.5

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.13

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