Variant rs8176707 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000538324.2(ABO):c.203+102C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0899 in 1,128,078 control chromosomes in the GnomAD database, including 5,089 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.075 ( 542 hom., cov: 33)

Exomes 𝑓: 0.092 ( 4547 hom. )

Consequence

ABO
ENST00000538324.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: 0.0440

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=-0.9).

BP6

Variant 9-133259717-G-T is Benign according to our data. Variant chr9-133259717-G-T is described in ClinVar as [Benign]. Clinvar id is 812633.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.106 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.203+102C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABO	ENST00000538324.2 linkuse as main transcript	c.203+102C>A		intron_variant		5		A2

Frequencies

GnomAD3 genomes

AF:

0.0753

AC:

11454

AN:

152102

Hom.:

543

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0221

Gnomad AMI

AF:

0.0890

Gnomad AMR

AF:

0.0937

Gnomad ASJ

AF:

0.0876

Gnomad EAS

AF:

0.114

Gnomad SAS

AF:

0.105

Gnomad FIN

AF:

0.0896

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0952

Gnomad OTH

AF:

0.0904

GnomAD4 exome

AF:

0.0922

AC:

89963

AN:

975858

Hom.:

4547

AF XY:

0.0921

AC XY:

46270

AN XY:

502436

show subpopulations

Gnomad4 AFR exome

AF:

0.0185

Gnomad4 AMR exome

AF:

0.115

Gnomad4 ASJ exome

AF:

0.0810

Gnomad4 EAS exome

AF:

0.0924

Gnomad4 SAS exome

AF:

0.0916

Gnomad4 FIN exome

AF:

0.0889

Gnomad4 NFE exome

AF:

0.0944

Gnomad4 OTH exome

AF:

0.0921

GnomAD4 genome

AF:

0.0752

AC:

11453

AN:

152220

Hom.:

542

Cov.:

AF XY:

0.0776

AC XY:

5776

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.0220

Gnomad4 AMR

AF:

0.0935

Gnomad4 ASJ

AF:

0.0876

Gnomad4 EAS

AF:

0.114

Gnomad4 SAS

AF:

0.104

Gnomad4 FIN

AF:

0.0896

Gnomad4 NFE

AF:

0.0952

Gnomad4 OTH

AF:

0.0909

Alfa

AF:

0.0868

Hom.:

101

Bravo

AF:

0.0744

Asia WGS

AF:

0.113

AC:

393

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Three Vessel Coronary Disease

Benign:1

Benign, no assertion criteria provided

clinical testing

Department of Cardiology, Chinese Academy of Medical Sciences, Fuwai Hospital

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.0

DANN

Benign

0.81

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over