Variant chr9-133257486-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_020469.3(ABO):c.294A>G(p.Thr98Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 1,612,622 control chromosomes in the GnomAD database, including 108,236 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as no classification for the single variant (no stars).

Frequency

Genomes: 𝑓 0.40 ( 12422 hom., cov: 31)

Exomes 𝑓: 0.36 ( 95814 hom. )

Consequence

ABO
NM_020469.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.49

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP7

Synonymous conserved (PhyloP=-1.49 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.469 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.294A>G	p.Thr98Thr	synonymous_variant	7/8		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.294A>G	p.Thr98Thr	synonymous_variant	7/9	5		ENSP00000483018.1		A0A087X009

Frequencies

GnomAD3 genomes

AF:

0.398

AC:

60103

AN:

151066

Hom.:

12399

Cov.:

show subpopulations

Gnomad AFR

AF:

0.462

Gnomad AMI

AF:

0.232

Gnomad AMR

AF:

0.477

Gnomad ASJ

AF:

0.416

Gnomad EAS

AF:

0.456

Gnomad SAS

AF:

0.480

Gnomad FIN

AF:

0.334

Gnomad MID

AF:

0.331

Gnomad NFE

AF:

0.344

Gnomad OTH

AF:

0.377

GnomAD3 exomes

AF:

0.404

AC:

100688

AN:

249194

Hom.:

21539

AF XY:

0.399

AC XY:

53910

AN XY:

135200

show subpopulations

Gnomad AFR exome

AF:

0.470

Gnomad AMR exome

AF:

0.557

Gnomad ASJ exome

AF:

0.403

Gnomad EAS exome

AF:

0.448

Gnomad SAS exome

AF:

0.475

Gnomad FIN exome

AF:

0.334

Gnomad NFE exome

AF:

0.337

Gnomad OTH exome

AF:

0.378

GnomAD4 exome

AF:

0.356

AC:

520743

AN:

1461438

Hom.:

95814

Cov.:

AF XY:

0.358

AC XY:

260430

AN XY:

727008

show subpopulations

Gnomad4 AFR exome

AF:

0.465

Gnomad4 AMR exome

AF:

0.544

Gnomad4 ASJ exome

AF:

0.409

Gnomad4 EAS exome

AF:

0.441

Gnomad4 SAS exome

AF:

0.473

Gnomad4 FIN exome

AF:

0.333

Gnomad4 NFE exome

AF:

0.332

Gnomad4 OTH exome

AF:

0.378

GnomAD4 genome

AF:

0.398

AC:

60160

AN:

151184

Hom.:

12422

Cov.:

AF XY:

0.401

AC XY:

29632

AN XY:

73858

show subpopulations

Gnomad4 AFR

AF:

0.462

Gnomad4 AMR

AF:

0.478

Gnomad4 ASJ

AF:

0.416

Gnomad4 EAS

AF:

0.455

Gnomad4 SAS

AF:

0.481

Gnomad4 FIN

AF:

0.334

Gnomad4 NFE

AF:

0.343

Gnomad4 OTH

AF:

0.374

Alfa

AF:

0.364

Hom.:

13744

Bravo

AF:

0.408

Asia WGS

AF:

0.472

AC:

1640

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

2.6

DANN

Benign

0.37

RBP_binding_hub_radar

1.0

RBP_regulation_power_radar

2.3

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