rs8176707

chr9-133259717-G-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The NM_020469.3(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 (no stars).

• Frequency:
  • Genomes: 𝑓 0.075 (542 hom., cov: 33)
  • Exomes 𝑓: 0.092 (4547 hom.)
• Consequence: ABO NM_020469.3 intron
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: 0.0440

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]

ACMG classification

Verdict is Benign. Variant got -13 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 no_assertion_criteria_provided, 0 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	c.203+102C>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0753 AC: 11454 AN: 152102 Hom.: 543 Cov.: 33

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

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.: 33 AF XY: 0.0776 AC XY: 5776 AN XY: 74422

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:1

Revision: no assertion criteria provided

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

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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

Other links and lift over

dbSNP: rs8176707; hg19: chr9-136135108; COSMIC: COSV71743469;