rs660340

Variant names:

• chr9-133272138-G-A
• rs660340
• ENST00000611156.4:c.28+3024C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-133272138-G-A
• chr9-133272138-G-C
• chr9-133272138-G-T

Variant summary

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

The ENST00000611156.4(ABO):​c.28+3024C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 152,022 control chromosomes in the GnomAD database, including 17,219 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 0.47 (17219 hom., cov: 32)
• Consequence: ABO ENST00000611156.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843
• Publications: 13 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABO	NR_198898.1	n.40+3024C>T		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABO	ENST00000611156.4	c.28+3024C>T		intron_variant	Intron 1 of 7	5		ENSP00000483265.1

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71806 AN: 151904 Hom.: 17195 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.473 AC: 71868 AN: 152022 Hom.: 17219 Cov.: 32 AF XY: 0.474 AC XY: 35204 AN XY: 74298

African (AFR) AF: 0.507 AC: 21005 AN: 41442

American (AMR) AF: 0.575 AC: 8790 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1479 AN: 3466

East Asian (EAS) AF: 0.495 AC: 2562 AN: 5178

South Asian (SAS) AF: 0.443 AC: 2136 AN: 4824

European-Finnish (FIN) AF: 0.391 AC: 4130 AN: 10550

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.447 AC: 30411 AN: 67978

Other (OTH) AF: 0.468 AC: 988 AN: 2112

Alfa AF: 0.475 Hom.: 2244

Bravo AF: 0.493

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs660340; hg19: chr9-136147553;