chr9-133256085-A-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_020469.3(ABO):c.643T>A(p.Phe215Ile) variant causes a missense change. The variant allele was found at a frequency of 0.243 in 1,588,528 control chromosomes in the GnomAD database, including 49,184 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.25 ( 5124 hom., cov: 33)
Exomes 𝑓: 0.24 ( 44060 hom. )
Consequence
ABO
NM_020469.3 missense
NM_020469.3 missense
Scores
3
6
Clinical Significance
Conservation
PhyloP100: 5.15
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
Computational evidence support a benign effect (MetaRNN=0.0047952533).
BP6
Variant 9-133256085-A-T is Benign according to our data. Variant chr9-133256085-A-T is described in ClinVar as [Benign]. Clinvar id is 812632.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-133256085-A-T is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABO | NM_020469.3 | c.643T>A | p.Phe215Ile | missense_variant | 8/8 | NP_065202.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABO | ENST00000538324.2 | c.643T>A | p.Phe215Ile | missense_variant | 8/9 | 5 | ENSP00000483018 | A2 |
Frequencies
GnomAD3 genomes AF: 0.251 AC: 38057AN: 151686Hom.: 5118 Cov.: 33
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GnomAD3 exomes AF: 0.253 AC: 52729AN: 208400Hom.: 7677 AF XY: 0.241 AC XY: 27333AN XY: 113208
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GnomAD4 exome AF: 0.243 AC: 348446AN: 1436724Hom.: 44060 Cov.: 72 AF XY: 0.239 AC XY: 170641AN XY: 712918
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GnomAD4 genome AF: 0.251 AC: 38079AN: 151804Hom.: 5124 Cov.: 33 AF XY: 0.251 AC XY: 18625AN XY: 74208
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Three Vessel Coronary Disease Benign:1
Benign, no assertion criteria provided | clinical testing | Department of Cardiology, Chinese Academy of Medical Sciences, Fuwai Hospital | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;.
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
PrimateAI
Uncertain
T
Sift4G
Uncertain
D;D
Vest4
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
gMVP
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at