dbSNP rs485186: FUT2:p.Thr331Thr (chr19-48703949-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_000511.6(FUT2):c.993A>G(p.Thr331Thr) 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

Publications

52 publications found

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:

LOC105447645 (HGNC:):

LOC105447645 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FUT2	NM_000511.6 link	c.993A>G	p.Thr331Thr	synonymous_variant	Exon 2 of 2	ENST00000425340.3	NP_000502.4	Q10981A8K2L2
FUT2	NM_001097638.3 link	c.993A>G	p.Thr331Thr	synonymous_variant	Exon 2 of 2		NP_001091107.1	Q10981A8K2L2
LOC105447645	NR_131188.1 link	n.-101T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FUT2	ENST00000425340.3 link	c.993A>G	p.Thr331Thr	synonymous_variant	Exon 2 of 2	1	NM_000511.6	ENSP00000387498.2		Q10981
FUT2	ENST00000522966.2 link	c.993A>G	p.Thr331Thr	synonymous_variant	Exon 2 of 2	2		ENSP00000430227.2		Q10981

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

GnomAD2 exomes

AF:

0.405

AC:

101715

AN:

250982

AF XY:

0.409

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 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

African (AFR)

AF:

0.511

AC:

17098

AN:

33476

American (AMR)

AF:

0.293

AC:

13089

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.472

AC:

12336

AN:

26130

East Asian (EAS)

AF:

0.00174

AC:

AN:

39626

South Asian (SAS)

AF:

0.322

AC:

27685

AN:

85874

European-Finnish (FIN)

AF:

0.422

AC:

22482

AN:

53334

Middle Eastern (MID)

AF:

0.540

AC:

3113

AN:

5768

European-Non Finnish (NFE)

AF:

0.526

AC:

584965

AN:

1111790

Other (OTH)

AF:

0.486

AC:

29329

AN:

60344

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

20733

41467

62200

82934

103667

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16506

33012

49518

66024

82530

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.463

AC:

70295

AN:

151936

Hom.:

17310

Cov.:

AF XY:

0.451

AC XY:

33469

AN XY:

74246

show subpopulations

African (AFR)

AF:

0.509

AC:

21103

AN:

41464

American (AMR)

AF:

0.386

AC:

5885

AN:

15240

Ashkenazi Jewish (ASJ)

AF:

0.471

AC:

1635

AN:

3468

East Asian (EAS)

AF:

0.00387

AC:

AN:

5172

South Asian (SAS)

AF:

0.297

AC:

1402

AN:

4726

European-Finnish (FIN)

AF:

0.411

AC:

4342

AN:

10562

Middle Eastern (MID)

AF:

0.585

AC:

172

AN:

294

European-Non Finnish (NFE)

AF:

0.506

AC:

34424

AN:

67996

Other (OTH)

AF:

0.470

AC:

988

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1852

3704

5557

7409

9261

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

616

1232

1848

2464

3080

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.490

Hom.:

45070

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

University of Washington Center for Mendelian Genomics, University of Washington

Significance:confers sensitivity

Review Status:no assertion criteria provided

Collection Method:research

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.27

(source)

DANN

Benign

0.39

PhyloP100

-1.9

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over