rs643434

Variant names:

• chr9-133266942-A-G
• rs643434
• ENST00000611156.4:c.29-4774T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-133266942-A-G
• chr9-133266942-A-T

Variant summary

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

The ENST00000611156.4(ABO):​c.29-4774T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 152,002 control chromosomes in the GnomAD database, including 27,728 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 0.60 (27728 hom., cov: 31)
• Consequence: ABO ENST00000611156.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 76 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000611156.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABO	NR_198898.1		n.41-4774T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABO	ENST00000611156.4	TSL:5	c.29-4774T>C		intron	N/A	ENSP00000483265.1	A0A087X0C2
	ABO	ENST00000453660.4	TSL:1	n.59-4774T>C		intron	N/A
	ABO	ENST00000538324.2	TSL:5	c.29-4774T>C		intron	N/A	ENSP00000483018.1	A0A087X009

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91258 AN: 151884 Hom.: 27706 Cov.: 31

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.601 AC: 91321 AN: 152002 Hom.: 27728 Cov.: 31 AF XY: 0.599 AC XY: 44524 AN XY: 74278

African (AFR) AF: 0.544 AC: 22556 AN: 41448

American (AMR) AF: 0.698 AC: 10668 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1977 AN: 3472

East Asian (EAS) AF: 0.615 AC: 3179 AN: 5170

South Asian (SAS) AF: 0.555 AC: 2667 AN: 4808

European-Finnish (FIN) AF: 0.522 AC: 5501 AN: 10536

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43001 AN: 67966

Other (OTH) AF: 0.618 AC: 1303 AN: 2110

Alfa AF: 0.617 Hom.: 47557

Bravo AF: 0.615

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs643434; hg19: chr9-136142355;