Genetic Variant FUT2:p.Ala68Ala (chr19-48703160-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.204A>G(p.Ala68Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 1,613,034 control chromosomes in the GnomAD database, including 179,898 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 0.44 ( 15739 hom., cov: 32)

Exomes 𝑓: 0.46 ( 164159 hom. )

Consequence

FUT2
NM_000511.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.88

Publications

177 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:

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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=-1.02).

BP7

Synonymous conserved (PhyloP=-4.88 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein
FUT2	NM_000511.6 link	c.204A>G	p.Ala68Ala	synonymous_variant	Exon 2 of 2	ENST00000425340.3	NP_000502.4
FUT2	NM_001097638.3 link	c.204A>G	p.Ala68Ala	synonymous_variant	Exon 2 of 2		NP_001091107.1
LOC105447645	NR_131188.1 link	n.689T>C		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FUT2	ENST00000425340.3 link	c.204A>G	p.Ala68Ala	synonymous_variant	Exon 2 of 2	1	NM_000511.6	ENSP00000387498.2
FUT2	ENST00000522966.2 link	c.204A>G	p.Ala68Ala	synonymous_variant	Exon 2 of 2	2		ENSP00000430227.2

Frequencies

GnomAD3 genomes

AF:

0.441

AC:

67006

AN:

151824

Hom.:

15746

Cov.:

show subpopulations

Gnomad AFR

AF:

0.499

Gnomad AMI

AF:

0.351

Gnomad AMR

AF:

0.369

Gnomad ASJ

AF:

0.443

Gnomad EAS

AF:

0.00409

Gnomad SAS

AF:

0.295

Gnomad FIN

AF:

0.368

Gnomad MID

AF:

0.566

Gnomad NFE

AF:

0.477

Gnomad OTH

AF:

0.459

GnomAD2 exomes

AF:

0.383

AC:

95977

AN:

250706

AF XY:

0.387

show subpopulations

Gnomad AFR exome

AF:

0.498

Gnomad AMR exome

AF:

0.264

Gnomad ASJ exome

AF:

0.449

Gnomad EAS exome

AF:

0.00268

Gnomad FIN exome

AF:

0.374

Gnomad NFE exome

AF:

0.476

Gnomad OTH exome

AF:

0.430

GnomAD4 exome

AF:

0.460

AC:

671822

AN:

1461094

Hom.:

164159

Cov.:

AF XY:

0.455

AC XY:

330623

AN XY:

726808

show subpopulations

African (AFR)

AF:

0.500

AC:

16736

AN:

33480

American (AMR)

AF:

0.276

AC:

12345

AN:

44676

Ashkenazi Jewish (ASJ)

AF:

0.444

AC:

11603

AN:

26134

East Asian (EAS)

AF:

0.00175

AC:

AN:

39522

South Asian (SAS)

AF:

0.319

AC:

27400

AN:

85880

European-Finnish (FIN)

AF:

0.376

AC:

20097

AN:

53380

Middle Eastern (MID)

AF:

0.511

AC:

2949

AN:

5766

European-Non Finnish (NFE)

AF:

0.497

AC:

552718

AN:

1111918

Other (OTH)

AF:

0.462

AC:

27905

AN:

60338

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

23197

46394

69592

92789

115986

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15924

31848

47772

63696

79620

<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:

0.441

AC:

67009

AN:

151940

Hom.:

15739

Cov.:

AF XY:

0.429

AC XY:

31852

AN XY:

74228

show subpopulations

African (AFR)

AF:

0.498

AC:

20668

AN:

41474

American (AMR)

AF:

0.368

AC:

5619

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.443

AC:

1538

AN:

3472

East Asian (EAS)

AF:

0.00410

AC:

AN:

5120

South Asian (SAS)

AF:

0.294

AC:

1390

AN:

4722

European-Finnish (FIN)

AF:

0.368

AC:

3893

AN:

10592

Middle Eastern (MID)

AF:

0.541

AC:

159

AN:

294

European-Non Finnish (NFE)

AF:

0.477

AC:

32446

AN:

67980

Other (OTH)

AF:

0.453

AC:

956

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1877

3754

5631

7508

9385

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

596

1192

1788

2384

2980

<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:

0.456

Hom.:

47790

Bravo

AF:

0.444

Asia WGS

AF:

0.141

AC:

488

AN:

3420

EpiCase

AF:

0.479

EpiControl

AF:

0.480

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.14

(source)

DANN

Benign

0.25

PhyloP100

-4.9

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

Computational scores

Splicing

Publications

Other links and lift over