rs7469576

Variant names:

• chr9-133242577-G-A
• rs7469576
• ENST00000679909.1:c.29-8968C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-133242577-G-A
• chr9-133242577-G-T

Variant summary

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

The ENST00000679909.1(ABO):​c.29-8968C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,138 control chromosomes in the GnomAD database, including 7,284 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 0.28 (7284 hom., cov: 32)
• Consequence: ABO ENST00000679909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.523
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000679909.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABO	ENST00000679909.1		c.29-8968C>T		intron	N/A	ENSP00000506089.1	A0A7P0TA91

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42322 AN: 152020 Hom.: 7264 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.279 AC: 42389 AN: 152138 Hom.: 7284 Cov.: 32 AF XY: 0.282 AC XY: 20982 AN XY: 74380

African (AFR) AF: 0.473 AC: 19602 AN: 41482

American (AMR) AF: 0.181 AC: 2761 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 699 AN: 3470

East Asian (EAS) AF: 0.346 AC: 1794 AN: 5182

South Asian (SAS) AF: 0.381 AC: 1840 AN: 4824

European-Finnish (FIN) AF: 0.258 AC: 2731 AN: 10572

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12109 AN: 68004

Other (OTH) AF: 0.247 AC: 523 AN: 2116

Alfa AF: 0.230 Hom.: 5184

Bravo AF: 0.275

Asia WGS AF: 0.369 AC: 1282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
DANN	Benign	0.83
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs7469576; hg19: chr9-136117964;