Variant rs485186 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_000511.6(FUT2):c.993A>G(p.Thr331=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 1,613,000 control chromosomes in the GnomAD database, including 200,381 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as confers sensitivity (no stars).

Frequency

Genomes: 𝑓 0.46 ( 17310 hom., cov: 31)

Exomes 𝑓: 0.49 ( 183071 hom. )

Consequence

FUT2
NM_000511.6 synonymous

Scores

Clinical Significance

confers sensitivity no assertion criteria provided O:1

Conservation

PhyloP100: -1.91

Variant links:

Genes affected

FUT2 (HGNC:4013): (fucosyltransferase 2 (H blood group)) This gene is one of two encoding the galactoside 2-L-fucosyltransferase enzyme. The encoded protein is important for the final step in the soluble ABO blood group antigen synthesis pathway. It is also involved in cell-cell interaction, cell surface expression, and cell proliferation. Mutations in this gene are a cause of the H-Bombay blood group where red blood cells lack the H antigen. [provided by RefSeq, May 2022]

FUT2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BP7

Synonymous conserved (PhyloP=-1.91 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FUT2	NM_000511.6 linkuse as main transcript	c.993A>G	p.Thr331=	synonymous_variant	2/2	ENST00000425340.3	NP_000502.4
FUT2	NM_001097638.3 linkuse as main transcript	c.993A>G	p.Thr331=	synonymous_variant	2/2		NP_001091107.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FUT2	ENST00000425340.3 linkuse as main transcript	c.993A>G	p.Thr331=	synonymous_variant	2/2	1	NM_000511.6	ENSP00000387498	P1
FUT2	ENST00000522966.2 linkuse as main transcript	c.993A>G	p.Thr331=	synonymous_variant	2/2	2		ENSP00000430227	P1

Frequencies

GnomAD3 genomes

AF:

0.463

AC:

70290

AN:

151822

Hom.:

17317

Cov.:

show subpopulations

Gnomad AFR

AF:

0.509

Gnomad AMI

AF:

0.355

Gnomad AMR

AF:

0.387

Gnomad ASJ

AF:

0.471

Gnomad EAS

AF:

0.00386

Gnomad SAS

AF:

0.297

Gnomad FIN

AF:

0.411

Gnomad MID

AF:

0.604

Gnomad NFE

AF:

0.506

Gnomad OTH

AF:

0.476

GnomAD3 exomes

AF:

0.405

AC:

101715

AN:

250982

Hom.:

23971

AF XY:

0.409

AC XY:

55459

AN XY:

135680

show subpopulations

Gnomad AFR exome

AF:

0.508

Gnomad AMR exome

AF:

0.280

Gnomad ASJ exome

AF:

0.476

Gnomad EAS exome

AF:

0.00251

Gnomad SAS exome

AF:

0.316

Gnomad FIN exome

AF:

0.419

Gnomad NFE exome

AF:

0.506

Gnomad OTH exome

AF:

0.456

GnomAD4 exome

AF:

0.486

AC:

710166

AN:

1461064

Hom.:

183071

Cov.:

AF XY:

0.481

AC XY:

349277

AN XY:

726778

show subpopulations

Gnomad4 AFR exome

AF:

0.511

Gnomad4 AMR exome

AF:

0.293

Gnomad4 ASJ exome

AF:

0.472

Gnomad4 EAS exome

AF:

0.00174

Gnomad4 SAS exome

AF:

0.322

Gnomad4 FIN exome

AF:

0.422

Gnomad4 NFE exome

AF:

0.526

Gnomad4 OTH exome

AF:

0.486

GnomAD4 genome

AF:

0.463

AC:

70295

AN:

151936

Hom.:

17310

Cov.:

AF XY:

0.451

AC XY:

33469

AN XY:

74246

show subpopulations

Gnomad4 AFR

AF:

0.509

Gnomad4 AMR

AF:

0.386

Gnomad4 ASJ

AF:

0.471

Gnomad4 EAS

AF:

0.00387

Gnomad4 SAS

AF:

0.297

Gnomad4 FIN

AF:

0.411

Gnomad4 NFE

AF:

0.506

Gnomad4 OTH

AF:

0.470

Alfa

AF:

0.494

Hom.:

31548

Bravo

AF:

0.464

Asia WGS

AF:

0.142

AC:

493

AN:

3416

EpiCase

AF:

0.507

EpiControl

AF:

0.510

ClinVar

Significance: confers sensitivity

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Familial Otitis Media

Other:1

confers sensitivity, no assertion criteria provided

research

University of Washington Center for Mendelian Genomics, University of Washington

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.27

DANN

Benign

0.39

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.

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