Variant rs8176741 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000538324.2(ABO):c.654C>T(p.His218=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0917 in 1,588,890 control chromosomes in the GnomAD database, including 9,425 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 0.12 ( 1298 hom., cov: 33)

Exomes 𝑓: 0.089 ( 8127 hom. )

Consequence

ABO
ENST00000538324.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.194

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP7

Synonymous conserved (PhyloP=-0.194 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.245 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.654C>T	p.His218=	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.654C>T	p.His218=	synonymous_variant	8/9	5		ENSP00000483018	A2

Frequencies

GnomAD3 genomes

AF:

0.115

AC:

17529

AN:

151920

Hom.:

1296

Cov.:

show subpopulations

Gnomad AFR

AF:

0.159

Gnomad AMI

AF:

0.0800

Gnomad AMR

AF:

0.0740

Gnomad ASJ

AF:

0.134

Gnomad EAS

AF:

0.183

Gnomad SAS

AF:

0.256

Gnomad FIN

AF:

0.137

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0798

Gnomad OTH

AF:

0.105

GnomAD3 exomes

AF:

0.119

AC:

24772

AN:

207772

Hom.:

2086

AF XY:

0.127

AC XY:

14330

AN XY:

112824

show subpopulations

Gnomad AFR exome

AF:

0.170

Gnomad AMR exome

AF:

0.0571

Gnomad ASJ exome

AF:

0.121

Gnomad EAS exome

AF:

0.185

Gnomad SAS exome

AF:

0.263

Gnomad FIN exome

AF:

0.137

Gnomad NFE exome

AF:

0.0775

Gnomad OTH exome

AF:

0.105

GnomAD4 exome

AF:

0.0892

AC:

128163

AN:

1436852

Hom.:

8127

Cov.:

AF XY:

0.0948

AC XY:

67607

AN XY:

712938

show subpopulations

Gnomad4 AFR exome

AF:

0.166

Gnomad4 AMR exome

AF:

0.0569

Gnomad4 ASJ exome

AF:

0.125

Gnomad4 EAS exome

AF:

0.181

Gnomad4 SAS exome

AF:

0.260

Gnomad4 FIN exome

AF:

0.135

Gnomad4 NFE exome

AF:

0.0680

Gnomad4 OTH exome

AF:

0.103

GnomAD4 genome

AF:

0.115

AC:

17543

AN:

152038

Hom.:

1298

Cov.:

AF XY:

0.120

AC XY:

8883

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.159

Gnomad4 AMR

AF:

0.0741

Gnomad4 ASJ

AF:

0.134

Gnomad4 EAS

AF:

0.183

Gnomad4 SAS

AF:

0.257

Gnomad4 FIN

AF:

0.137

Gnomad4 NFE

AF:

0.0798

Gnomad4 OTH

AF:

0.104

Alfa

AF:

0.0810

Hom.:

1041

Bravo

AF:

0.106

Asia WGS

AF:

0.197

AC:

683

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.6

DANN

Benign

0.86

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