9-133267960-T-C

Variant names:

• chr9-133267960-T-C
• rs545971
• ENST00000611156.4:c.29-5792A>G

Variant summary

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

The ENST00000611156.4(ABO):​c.29-5792A>G 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 151,854 control chromosomes in the GnomAD database, including 29,123 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 (29123 hom., cov: 31)
• Consequence: ABO ENST00000611156.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 39 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.704 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABO	NR_198898.1		n.41-5792A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABO	ENST00000611156.4	TSL:5	c.29-5792A>G		intron	N/A	ENSP00000483265.1
	ABO	ENST00000453660.4	TSL:1	n.59-5792A>G		intron	N/A
	ABO	ENST00000538324.2	TSL:5	c.29-5792A>G		intron	N/A	ENSP00000483018.1

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93488 AN: 151736 Hom.: 29101 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.616 AC: 93551 AN: 151854 Hom.: 29123 Cov.: 31 AF XY: 0.614 AC XY: 45562 AN XY: 74192

African (AFR) AF: 0.549 AC: 22690 AN: 41358

American (AMR) AF: 0.715 AC: 10929 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1992 AN: 3470

East Asian (EAS) AF: 0.614 AC: 3172 AN: 5166

South Asian (SAS) AF: 0.564 AC: 2723 AN: 4828

European-Finnish (FIN) AF: 0.539 AC: 5653 AN: 10494

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

European-Non Finnish (NFE) AF: 0.656 AC: 44544 AN: 67948

Other (OTH) AF: 0.632 AC: 1333 AN: 2108

Alfa AF: 0.597 Hom.: 6517

Bravo AF: 0.630

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs545971; hg19: chr9-136143372;