Variant 9-133256085-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The ENST00000538324.2(ABO):c.643T>A(p.Phe215Ile) variant causes a missense change. The variant allele was found at a frequency of 0.243 in 1,588,528 control chromosomes in the GnomAD database, including 49,184 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.25 ( 5124 hom., cov: 33)

Exomes 𝑓: 0.24 ( 44060 hom. )

Consequence

ABO
ENST00000538324.2 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 5.15

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0047952533).

BP6

Variant 9-133256085-A-T is Benign according to our data. Variant chr9-133256085-A-T is described in ClinVar as [Benign]. Clinvar id is 812632.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr9-133256085-A-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.372 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.643T>A	p.Phe215Ile	missense_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABO	ENST00000538324.2 linkuse as main transcript	c.643T>A	p.Phe215Ile	missense_variant	8/9	5		A2

Frequencies

GnomAD3 genomes

AF:

0.251

AC:

38057

AN:

151686

Hom.:

5118

Cov.:

show subpopulations

Gnomad AFR

AF:

0.244

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.379

Gnomad ASJ

AF:

0.277

Gnomad EAS

AF:

0.269

Gnomad SAS

AF:

0.212

Gnomad FIN

AF:

0.179

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.240

Gnomad OTH

AF:

0.244

GnomAD3 exomes

AF:

0.253

AC:

52729

AN:

208400

Hom.:

7677

AF XY:

0.241

AC XY:

27333

AN XY:

113208

show subpopulations

Gnomad AFR exome

AF:

0.233

Gnomad AMR exome

AF:

0.467

Gnomad ASJ exome

AF:

0.269

Gnomad EAS exome

AF:

0.244

Gnomad SAS exome

AF:

0.198

Gnomad FIN exome

AF:

0.172

Gnomad NFE exome

AF:

0.221

Gnomad OTH exome

AF:

0.245

GnomAD4 exome

AF:

0.243

AC:

348446

AN:

1436724

Hom.:

44060

Cov.:

AF XY:

0.239

AC XY:

170641

AN XY:

712918

show subpopulations

Gnomad4 AFR exome

AF:

0.240

Gnomad4 AMR exome

AF:

0.455

Gnomad4 ASJ exome

AF:

0.277

Gnomad4 EAS exome

AF:

0.254

Gnomad4 SAS exome

AF:

0.202

Gnomad4 FIN exome

AF:

0.175

Gnomad4 NFE exome

AF:

0.239

Gnomad4 OTH exome

AF:

0.251

GnomAD4 genome

AF:

0.251

AC:

38079

AN:

151804

Hom.:

5124

Cov.:

AF XY:

0.251

AC XY:

18625

AN XY:

74208

show subpopulations

Gnomad4 AFR

AF:

0.243

Gnomad4 AMR

AF:

0.380

Gnomad4 ASJ

AF:

0.277

Gnomad4 EAS

AF:

0.268

Gnomad4 SAS

AF:

0.211

Gnomad4 FIN

AF:

0.179

Gnomad4 NFE

AF:

0.240

Gnomad4 OTH

AF:

0.243

Alfa

AF:

0.244

Hom.:

1638

Bravo

AF:

0.269

TwinsUK

AF:

0.238

AC:

883

ALSPAC

AF:

0.247

AC:

953

ESP6500AA

AF:

0.221

AC:

958

ESP6500EA

AF:

0.229

AC:

1946

ExAC

AF:

0.213

AC:

25437

Asia WGS

AF:

0.261

AC:

907

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

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

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.38

BayesDel_noAF

Benign

-0.17

CADD

Benign

DANN

Benign

0.64

DEOGEN2

Benign

0.28

T;.

FATHMM_MKL

Uncertain

0.90

LIST_S2

Benign

0.75

T;T

MetaRNN

Benign

0.0048

T;T

PrimateAI

Uncertain

0.59

Sift4G

Uncertain

0.0020

D;D

Vest4

0.41

GERP RS

3.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

gMVP

0.62

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