rs505922
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020469.3(ABO):c.28+1349G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 151,990 control chromosomes in the GnomAD database, including 31,838 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 0.64 ( 31838 hom., cov: 31)
Consequence
ABO
NM_020469.3 intron
NM_020469.3 intron
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.571
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 was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABO | NM_020469.3 | c.28+1349G>A | intron_variant | Intron 1 of 7 | NP_065202.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABO | ENST00000538324.2 | c.28+1349G>A | intron_variant | Intron 1 of 8 | 5 | ENSP00000483018.1 |
Frequencies
GnomAD3 genomes AF: 0.645 AC: 97949AN: 151872Hom.: 31808 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
97949
AN:
151872
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.645 AC: 98024AN: 151990Hom.: 31838 Cov.: 31 AF XY: 0.642 AC XY: 47716AN XY: 74294 show subpopulations
GnomAD4 genome
AF:
AC:
98024
AN:
151990
Hom.:
Cov.:
31
AF XY:
AC XY:
47716
AN XY:
74294
Gnomad4 AFR
AF:
AC:
0.645287
AN:
0.645287
Gnomad4 AMR
AF:
AC:
0.726814
AN:
0.726814
Gnomad4 ASJ
AF:
AC:
0.588099
AN:
0.588099
Gnomad4 EAS
AF:
AC:
0.615385
AN:
0.615385
Gnomad4 SAS
AF:
AC:
0.56473
AN:
0.56473
Gnomad4 FIN
AF:
AC:
0.539182
AN:
0.539182
Gnomad4 NFE
AF:
AC:
0.656994
AN:
0.656994
Gnomad4 OTH
AF:
AC:
0.65545
AN:
0.65545
Heterozygous variant carriers
0
1758
3516
5275
7033
8791
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
794
1588
2382
3176
3970
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at