chr9-133266804-G-T

Variant names:

• chr9-133266804-G-T
• rs644234
• ENST00000611156.4:c.29-4636C>A

Variant summary

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

The ENST00000611156.4(ABO):​c.29-4636C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 150,900 control chromosomes in the GnomAD database, including 27,699 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 (27699 hom., cov: 33)
• Consequence: ABO ENST00000611156.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 53 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 (Cadd=0.204).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.694 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.41-4636C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABO	ENST00000611156.4	TSL:5	c.29-4636C>A		intron	N/A	ENSP00000483265.1	A0A087X0C2
	ABO	ENST00000453660.4	TSL:1	n.59-4636C>A		intron	N/A
	ABO	ENST00000538324.2	TSL:5	c.29-4636C>A		intron	N/A	ENSP00000483018.1	A0A087X009

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91223 AN: 150782 Hom.: 27677 Cov.: 33

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.605 AC: 91285 AN: 150900 Hom.: 27699 Cov.: 33 AF XY: 0.603 AC XY: 44527 AN XY: 73784

African (AFR) AF: 0.544 AC: 22519 AN: 41384

American (AMR) AF: 0.705 AC: 10658 AN: 15118

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1973 AN: 3460

East Asian (EAS) AF: 0.614 AC: 3183 AN: 5182

South Asian (SAS) AF: 0.558 AC: 2673 AN: 4794

European-Finnish (FIN) AF: 0.528 AC: 5505 AN: 10420

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

European-Non Finnish (NFE) AF: 0.639 AC: 43005 AN: 67276

Other (OTH) AF: 0.620 AC: 1302 AN: 2100

Alfa AF: 0.584 Hom.: 5567

Bravo AF: 0.614

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.20
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs644234;