Variant 9-133255635-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.1089G>A(p.Pro363Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 1,563,090 control chromosomes in the GnomAD database, including 12,030 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.13 ( 1558 hom., cov: 32)

Exomes 𝑓: 0.11 ( 10472 hom. )

Consequence

ABO
ENST00000538324.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.315

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:

ABO (HGNC:):

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=-0.87).

BP6

Variant 9-133255635-C-T is Benign according to our data. Variant chr9-133255635-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.315 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.255 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.*31G>A		3_prime_UTR_variant	8/8		NP_065202.2	P16442A0A089QDC1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABO	ENST00000538324.2 linkuse as main transcript	c.1089G>A	p.Pro363Pro	synonymous_variant	9/9	5		ENSP00000483018.1		A0A087X009

Frequencies

GnomAD3 genomes

AF:

0.131

AC:

19890

AN:

151760

Hom.:

1556

Cov.:

show subpopulations

Gnomad AFR

AF:

0.166

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.0913

Gnomad ASJ

AF:

0.138

Gnomad EAS

AF:

0.182

Gnomad SAS

AF:

0.266

Gnomad FIN

AF:

0.154

Gnomad MID

AF:

0.0828

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.119

GnomAD3 exomes

AF:

0.135

AC:

21981

AN:

163044

Hom.:

2007

AF XY:

0.144

AC XY:

12818

AN XY:

89166

show subpopulations

Gnomad AFR exome

AF:

0.165

Gnomad AMR exome

AF:

0.0672

Gnomad ASJ exome

AF:

0.125

Gnomad EAS exome

AF:

0.184

Gnomad SAS exome

AF:

0.269

Gnomad FIN exome

AF:

0.154

Gnomad NFE exome

AF:

0.0950

Gnomad OTH exome

AF:

0.128

GnomAD4 exome

AF:

0.109

AC:

153222

AN:

1411210

Hom.:

10472

Cov.:

AF XY:

0.114

AC XY:

79359

AN XY:

697916

show subpopulations

Gnomad4 AFR exome

AF:

0.171

Gnomad4 AMR exome

AF:

0.0687

Gnomad4 ASJ exome

AF:

0.129

Gnomad4 EAS exome

AF:

0.180

Gnomad4 SAS exome

AF:

0.271

Gnomad4 FIN exome

AF:

0.155

Gnomad4 NFE exome

AF:

0.0901

Gnomad4 OTH exome

AF:

0.121

GnomAD4 genome

AF:

0.131

AC:

19903

AN:

151880

Hom.:

1558

Cov.:

AF XY:

0.135

AC XY:

9994

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.166

Gnomad4 AMR

AF:

0.0914

Gnomad4 ASJ

AF:

0.138

Gnomad4 EAS

AF:

0.182

Gnomad4 SAS

AF:

0.267

Gnomad4 FIN

AF:

0.154

Gnomad4 NFE

AF:

0.102

Gnomad4 OTH

AF:

0.118

Alfa

AF:

0.128

Hom.:

301

Bravo

AF:

0.122

Asia WGS

AF:

0.206

AC:

714

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.6

DANN

Benign

0.63

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