Variant rs688976 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000538324.2(ABO):c.106G>T(p.Val36Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 1,594,332 control chromosomes in the GnomAD database, including 51,939 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/5 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.27 ( 5809 hom., cov: 32)

Exomes 𝑓: 0.25 ( 46130 hom. )

Consequence

ABO
ENST00000538324.2 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.461

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]

ABO links:

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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=0.002935797).

BP6

Variant 9-133261367-C-A is Benign according to our data. Variant chr9-133261367-C-A is described in ClinVar as [Benign]. Clinvar id is 769758.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABO	NM_020469.3 linkuse as main transcript	c.106G>T	p.Val36Phe	missense_variant	3/8		NP_065202.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABO	ENST00000538324.2 linkuse as main transcript	c.106G>T	p.Val36Phe	missense_variant	3/9	5		ENSP00000483018	A2

Frequencies

GnomAD3 genomes

AF:

0.270

AC:

41012

AN:

151998

Hom.:

5803

Cov.:

show subpopulations

Gnomad AFR

AF:

0.309

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.384

Gnomad ASJ

AF:

0.276

Gnomad EAS

AF:

0.271

Gnomad SAS

AF:

0.215

Gnomad FIN

AF:

0.178

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.241

Gnomad OTH

AF:

0.254

GnomAD4 exome

AF:

0.248

AC:

357039

AN:

1442216

Hom.:

46130

Cov.:

AF XY:

0.244

AC XY:

174731

AN XY:

715164

show subpopulations

Gnomad4 AFR exome

AF:

0.310

Gnomad4 AMR exome

AF:

0.475

Gnomad4 ASJ exome

AF:

0.279

Gnomad4 EAS exome

AF:

0.260

Gnomad4 SAS exome

AF:

0.206

Gnomad4 FIN exome

AF:

0.178

Gnomad4 NFE exome

AF:

0.242

Gnomad4 OTH exome

AF:

0.257

GnomAD4 genome

AF:

0.270

AC:

41039

AN:

152116

Hom.:

5809

Cov.:

AF XY:

0.269

AC XY:

19984

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.309

Gnomad4 AMR

AF:

0.385

Gnomad4 ASJ

AF:

0.276

Gnomad4 EAS

AF:

0.271

Gnomad4 SAS

AF:

0.215

Gnomad4 FIN

AF:

0.178

Gnomad4 NFE

AF:

0.241

Gnomad4 OTH

AF:

0.253

Alfa

AF:

0.243

Hom.:

7929

Bravo

AF:

0.291

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.82

DEOGEN2

Benign

0.0018

T;.

LIST_S2

Benign

0.46

T;T

MetaRNN

Benign

0.0029

T;T

Sift4G

Benign

0.65

T;T

Vest4

0.11

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

gMVP

0.41

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over