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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.571

Links

ABO (HGNC:79):

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
ABO	NM_020469.3 linkuse as main transcript	c.28+1349G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABO	ENST00000538324.2 linkuse as main transcript	c.28+1349G>A		intron_variant		5		A2

Frequencies

GnomAD3 genomes

AF:

0.645

AC:

97949

AN:

151872

Hom.:

31808

Cov.:

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.