rs2519093
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020469.3(ABO):c.29-4288A>G 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 151,838 control chromosomes in the GnomAD database, including 52,811 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 ( 52811 hom., cov: 29)
Consequence
ABO
NM_020469.3 intron
NM_020469.3 intron
Scores
1
Clinical Significance
Conservation
PhyloP100: -1.08
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABO | NM_020469.3 | c.29-4288A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABO | ENST00000538324.2 | c.29-4288A>G | intron_variant | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.832 AC: 126233AN: 151722Hom.: 52745 Cov.: 29
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.832 AC: 126357AN: 151838Hom.: 52811 Cov.: 29 AF XY: 0.834 AC XY: 61896AN XY: 74202
GnomAD4 genome
?
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126357
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29
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61896
AN XY:
74202
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ClinVar
Significance: association
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
ABO blood group system Other:1
association, no assertion criteria provided | research | Blood Transfusion Service Zurich, Swiss Red Cross | May 01, 2021 | ABO blood group system, phenotype A1, diagnostic specificity for ABO*A1.01 and ABO*A1.02 blood group alleles (rs2519093 A allele, NG_006669.2:g.13759A) - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at