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GeneBe

9-133255635-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The ENST00000538324.2(ABO):c.1089G>A(p.Pro363=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 1,563,090 control chromosomes in the GnomAD database, including 12,030 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.13 ( 1558 hom., cov: 32)
Exomes 𝑓: 0.11 ( 10472 hom. )

Consequence

ABO
ENST00000538324.2 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.315
Variant links:
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 -14 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 9-133255635-C-T is Benign according to our data. Variant chr9-133255635-C-T is described in Lovd as [Benign].
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.315 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ABONM_020469.3 linkuse as main transcriptc.*31G>A 3_prime_UTR_variant 8/8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ABOENST00000538324.2 linkuse as main transcriptc.1089G>A p.Pro363= synonymous_variant 9/95 A2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.131
AC:
19890
AN:
151760
Hom.:
1556
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.166
Gnomad AMI
AF:
0.127
Gnomad AMR
AF:
0.0913
Gnomad ASJ
AF:
0.138
Gnomad EAS
AF:
0.182
Gnomad SAS
AF:
0.266
Gnomad FIN
AF:
0.154
Gnomad MID
AF:
0.0828
Gnomad NFE
AF:
0.102
Gnomad OTH
AF:
0.119
GnomAD3 exomes
AF:
0.135
AC:
21981
AN:
163044
Hom.:
2007
AF XY:
0.144
AC XY:
12818
AN XY:
89166
show subpopulations
Gnomad AFR exome
AF:
0.165
Gnomad AMR exome
AF:
0.0672
Gnomad ASJ exome
AF:
0.125
Gnomad EAS exome
AF:
0.184
Gnomad SAS exome
AF:
0.269
Gnomad FIN exome
AF:
0.154
Gnomad NFE exome
AF:
0.0950
Gnomad OTH exome
AF:
0.128
GnomAD4 exome
AF:
0.109
AC:
153222
AN:
1411210
Hom.:
10472
Cov.:
46
AF XY:
0.114
AC XY:
79359
AN XY:
697916
show subpopulations
Gnomad4 AFR exome
AF:
0.171
Gnomad4 AMR exome
AF:
0.0687
Gnomad4 ASJ exome
AF:
0.129
Gnomad4 EAS exome
AF:
0.180
Gnomad4 SAS exome
AF:
0.271
Gnomad4 FIN exome
AF:
0.155
Gnomad4 NFE exome
AF:
0.0901
Gnomad4 OTH exome
AF:
0.121
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.131
AC:
19903
AN:
151880
Hom.:
1558
Cov.:
32
AF XY:
0.135
AC XY:
9994
AN XY:
74262
show subpopulations
Gnomad4 AFR
AF:
0.166
Gnomad4 AMR
AF:
0.0914
Gnomad4 ASJ
AF:
0.138
Gnomad4 EAS
AF:
0.182
Gnomad4 SAS
AF:
0.267
Gnomad4 FIN
AF:
0.154
Gnomad4 NFE
AF:
0.102
Gnomad4 OTH
AF:
0.118
Alfa
AF:
0.128
Hom.:
301
Bravo
AF:
0.122
Asia WGS
AF:
0.206
AC:
714
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
Cadd
Benign
1.6
Dann
Benign
0.63
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs8176751; hg19: chr9-136131022; API