ENST00000611156.4:c.28+1179T>C

Variant names:

• chr9-133273983-A-G
• rs507666
• ENST00000611156.4:c.28+1179T>C

Variant summary

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

The ENST00000611156.4(ABO):​c.28+1179T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 152,082 control chromosomes in the GnomAD database, including 52,825 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.83 (52825 hom., cov: 30)
• Consequence: ABO ENST00000611156.4 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -0.162
• Publications: 133 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.886 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.40+1179T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABO	ENST00000611156.4	TSL:5	c.28+1179T>C		intron	N/A	ENSP00000483265.1
	ABO	ENST00000453660.4	TSL:1	n.58+1179T>C		intron	N/A
	ABO	ENST00000538324.2	TSL:5	c.28+1179T>C		intron	N/A	ENSP00000483018.1

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126350 AN: 151964 Hom.: 52759 Cov.: 30

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.832 AC: 126475 AN: 152082 Hom.: 52825 Cov.: 30 AF XY: 0.834 AC XY: 61976 AN XY: 74346

African (AFR) AF: 0.894 AC: 37084 AN: 41490

American (AMR) AF: 0.848 AC: 12961 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2738 AN: 3470

East Asian (EAS) AF: 0.796 AC: 4107 AN: 5158

South Asian (SAS) AF: 0.845 AC: 4066 AN: 4812

European-Finnish (FIN) AF: 0.791 AC: 8361 AN: 10574

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.804 AC: 54668 AN: 67978

Other (OTH) AF: 0.826 AC: 1745 AN: 2112

Alfa AF: 0.810 Hom.: 147012

Bravo AF: 0.837

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

ABO blood group system Other:1

May 01, 2021

Blood Transfusion Service Zurich, Swiss Red Cross

Significance: association

Review Status: no assertion criteria provided

Collection Method: research

ABO blood group system, phenotype A1, diagnostic specificity for ABO*A1.01 and ABO*A1.02 blood group alleles (rs507666 T allele, NG_006669.2:g.6232T)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs507666; hg19: chr9-136149399;