rs638756

Variant names:

• chr9-133259081-A-C
• rs638756
• ENST00000611156.4:c.203+738T>G

Your query was ambiguous. Multiple possible variants found:

• chr9-133259081-A-C
• chr9-133259081-A-G

Variant summary

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

The ENST00000611156.4(ABO):​c.203+738T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,054 control chromosomes in the GnomAD database, including 6,250 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 (6250 hom., cov: 32)
• Consequence: ABO ENST00000611156.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• Publications: 11 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 (AMR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABO	NR_198898.1	n.215+738T>G		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABO	ENST00000611156.4	c.203+738T>G		intron_variant	Intron 4 of 7	5		ENSP00000483265.1

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42294 AN: 151938 Hom.: 6238 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.278 AC: 42337 AN: 152054 Hom.: 6250 Cov.: 32 AF XY: 0.277 AC XY: 20593 AN XY: 74328

African (AFR) AF: 0.338 AC: 14033 AN: 41476

American (AMR) AF: 0.388 AC: 5930 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 959 AN: 3470

East Asian (EAS) AF: 0.275 AC: 1421 AN: 5158

South Asian (SAS) AF: 0.215 AC: 1036 AN: 4826

European-Finnish (FIN) AF: 0.178 AC: 1880 AN: 10582

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16355 AN: 67954

Other (OTH) AF: 0.262 AC: 553 AN: 2110

Alfa AF: 0.268 Hom.: 1755

Bravo AF: 0.301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs638756; hg19: chr9-136134472;