rs674302

Variant names:

• chr9-133271249-A-T
• rs674302
• ENST00000611156.4:c.28+3913T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000611156.4(ABO):​c.28+3913T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 151,632 control chromosomes in the GnomAD database, including 29,108 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.62 (29108 hom., cov: 30)
• Consequence: ABO ENST00000611156.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 31 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABO	NR_198898.1	n.40+3913T>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABO	ENST00000611156.4	c.28+3913T>A		intron_variant	Intron 1 of 7	5		ENSP00000483265.1

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93415 AN: 151518 Hom.: 29087 Cov.: 30

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.631

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.616 AC: 93474 AN: 151632 Hom.: 29108 Cov.: 30 AF XY: 0.615 AC XY: 45543 AN XY: 74086

African (AFR) AF: 0.549 AC: 22659 AN: 41310

American (AMR) AF: 0.716 AC: 10923 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1990 AN: 3462

East Asian (EAS) AF: 0.616 AC: 3169 AN: 5148

South Asian (SAS) AF: 0.564 AC: 2707 AN: 4798

European-Finnish (FIN) AF: 0.540 AC: 5660 AN: 10474

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.656 AC: 44521 AN: 67880

Other (OTH) AF: 0.633 AC: 1330 AN: 2100

Alfa AF: 0.632 Hom.: 3764

Bravo AF: 0.630

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
PhyloP100		-1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs674302; hg19: chr9-136146664;