rs630014

Variant names:

• chr9-133274306-G-A
• rs630014
• ENST00000611156.4:c.28+856C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-133274306-G-A
• chr9-133274306-G-C
• chr9-133274306-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+856C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 151,964 control chromosomes in the GnomAD database, including 15,900 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 0.45 (15900 hom., cov: 32)
• Consequence: ABO ENST00000611156.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 61 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABO	NR_198898.1	n.40+856C>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+856C>T		intron_variant	Intron 1 of 7	5		ENSP00000483265.1

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68776 AN: 151844 Hom.: 15890 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.453 AC: 68814 AN: 151964 Hom.: 15900 Cov.: 32 AF XY: 0.448 AC XY: 33290 AN XY: 74250

African (AFR) AF: 0.435 AC: 18031 AN: 41432

American (AMR) AF: 0.551 AC: 8422 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1536 AN: 3468

East Asian (EAS) AF: 0.411 AC: 2114 AN: 5146

South Asian (SAS) AF: 0.346 AC: 1668 AN: 4818

European-Finnish (FIN) AF: 0.344 AC: 3631 AN: 10558

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32076 AN: 67948

Other (OTH) AF: 0.460 AC: 971 AN: 2110

Alfa AF: 0.468 Hom.: 59591

Bravo AF: 0.472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.54
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs630014; hg19: chr9-136149722;