Variant chr9-133256050-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The ENST00000538324.2(ABO):c.678G>A(p.Pro226=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 1,584,234 control chromosomes in the GnomAD database, including 47,228 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.22 ( 4250 hom., cov: 33)

Exomes 𝑓: 0.24 ( 42978 hom. )

Consequence

ABO
ENST00000538324.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.34

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 9-133256050-C-T is Benign according to our data. Variant chr9-133256050-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-1.34 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABO	NM_020469.3 linkuse as main transcript	c.678G>A	p.Pro226=	synonymous_variant	8/8		NP_065202.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABO	ENST00000538324.2 linkuse as main transcript	c.678G>A	p.Pro226=	synonymous_variant	8/9	5		ENSP00000483018	A2

Frequencies

GnomAD3 genomes

AF:

0.223

AC:

33859

AN:

151818

Hom.:

4245

Cov.:

show subpopulations

Gnomad AFR

AF:

0.147

Gnomad AMI

AF:

0.102

Gnomad AMR

AF:

0.369

Gnomad ASJ

AF:

0.275

Gnomad EAS

AF:

0.267

Gnomad SAS

AF:

0.210

Gnomad FIN

AF:

0.179

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.240

Gnomad OTH

AF:

0.229

GnomAD3 exomes

AF:

0.245

AC:

49369

AN:

201662

Hom.:

7081

AF XY:

0.234

AC XY:

25628

AN XY:

109470

show subpopulations

Gnomad AFR exome

AF:

0.136

Gnomad AMR exome

AF:

0.458

Gnomad ASJ exome

AF:

0.269

Gnomad EAS exome

AF:

0.244

Gnomad SAS exome

AF:

0.196

Gnomad FIN exome

AF:

0.171

Gnomad NFE exome

AF:

0.218

Gnomad OTH exome

AF:

0.239

GnomAD4 exome

AF:

0.239

AC:

342966

AN:

1432298

Hom.:

42978

Cov.:

AF XY:

0.237

AC XY:

168124

AN XY:

710358

show subpopulations

Gnomad4 AFR exome

AF:

0.139

Gnomad4 AMR exome

AF:

0.447

Gnomad4 ASJ exome

AF:

0.277

Gnomad4 EAS exome

AF:

0.255

Gnomad4 SAS exome

AF:

0.201

Gnomad4 FIN exome

AF:

0.175

Gnomad4 NFE exome

AF:

0.239

Gnomad4 OTH exome

AF:

0.245

GnomAD4 genome

AF:

0.223

AC:

33872

AN:

151936

Hom.:

4250

Cov.:

AF XY:

0.223

AC XY:

16581

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.147

Gnomad4 AMR

AF:

0.370

Gnomad4 ASJ

AF:

0.275

Gnomad4 EAS

AF:

0.267

Gnomad4 SAS

AF:

0.209

Gnomad4 FIN

AF:

0.179

Gnomad4 NFE

AF:

0.240

Gnomad4 OTH

AF:

0.227

Alfa

AF:

0.239

Hom.:

6252

Bravo

AF:

0.237

Asia WGS

AF:

0.256

AC:

889

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.1

DANN

Benign

0.72

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over