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GeneBe

rs505922

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020469(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 151872 control chromosomes in the gnomAD Genomes database, including 31808 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 ( 31808 hom., cov: 31)

Consequence

ABO
NM_020469 intron

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.571

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ABONM_020469.3 linkuse as main transcriptc.28+1349G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ABOENST00000538324.2 linkuse as main transcriptc.28+1349G>A intron_variant 5 A2

Frequencies

GnomAD3 genomes
AF:
0.645
AC:
97949
AN:
151872
Hom.:
31808
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.646
Gnomad AMI
AF:
0.356
Gnomad AMR
AF:
0.727
Gnomad ASJ
AF:
0.588
Gnomad EAS
AF:
0.615
Gnomad SAS
AF:
0.565
Gnomad FIN
AF:
0.539
Gnomad MID
AF:
0.665
Gnomad NFE
AF:
0.657
Gnomad OTH
AF:
0.653
Alfa
AF:
0.650
Hom.:
42754
Bravo
AF:
0.663

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
Cadd
Benign
2.0
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

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: rs505922; hg19: chr9-136149229;