Genetic Variant FUT2:c.-2-40C>T (chr19-48702915-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000511.6(FUT2):c.-2-40C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 1,604,928 control chromosomes in the GnomAD database, including 179,278 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 ( 15725 hom., cov: 32)

Exomes 𝑓: 0.46 ( 163553 hom. )

Consequence

FUT2
NM_000511.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.240

Publications

130 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
FUT2	NM_000511.6 link	c.-2-40C>T	intron_variant	Intron 1 of 1	ENST00000425340.3	NP_000502.4	Q10981A8K2L2
LOC105447645	NR_131188.1 link	n.934G>A	non_coding_transcript_exon_variant	Exon 1 of 1
FUT2	NM_001097638.3 link	c.-2-40C>T	intron_variant	Intron 1 of 1		NP_001091107.1	Q10981A8K2L2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FUT2	ENST00000425340.3 link	c.-2-40C>T		intron_variant	Intron 1 of 1	1	NM_000511.6	ENSP00000387498.2		Q10981
FUT2	ENST00000522966.2 link	c.-2-40C>T		intron_variant	Intron 1 of 1	2		ENSP00000430227.2		Q10981

Frequencies

GnomAD3 genomes

AF:

0.441

AC:

66959

AN:

151830

Hom.:

15732

Cov.:

show subpopulations

Gnomad AFR

AF:

0.498

Gnomad AMI

AF:

0.350

Gnomad AMR

AF:

0.369

Gnomad ASJ

AF:

0.444

Gnomad EAS

AF:

0.00369

Gnomad SAS

AF:

0.296

Gnomad FIN

AF:

0.367

Gnomad MID

AF:

0.582

Gnomad NFE

AF:

0.477

Gnomad OTH

AF:

0.457

GnomAD2 exomes

AF:

0.383

AC:

95557

AN:

249716

AF XY:

0.387

show subpopulations

Gnomad AFR exome

AF:

0.497

Gnomad AMR exome

AF:

0.265

Gnomad ASJ exome

AF:

0.451

Gnomad EAS exome

AF:

0.00295

Gnomad FIN exome

AF:

0.372

Gnomad NFE exome

AF:

0.475

Gnomad OTH exome

AF:

0.431

GnomAD4 exome

AF:

0.460

AC:

668503

AN:

1452982

Hom.:

163553

Cov.:

AF XY:

0.455

AC XY:

329249

AN XY:

723334

show subpopulations

African (AFR)

AF:

0.499

AC:

16650

AN:

33340

American (AMR)

AF:

0.277

AC:

12375

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.446

AC:

11646

AN:

26096

East Asian (EAS)

AF:

0.00185

AC:

AN:

39462

South Asian (SAS)

AF:

0.320

AC:

27261

AN:

85184

European-Finnish (FIN)

AF:

0.375

AC:

19486

AN:

51922

Middle Eastern (MID)

AF:

0.514

AC:

2958

AN:

5750

European-Non Finnish (NFE)

AF:

0.497

AC:

550290

AN:

1106520

Other (OTH)

AF:

0.463

AC:

27764

AN:

59990

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

19323

38647

57970

77294

96617

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15810

31620

47430

63240

79050

<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:

66963

AN:

151946

Hom.:

15725

Cov.:

AF XY:

0.429

AC XY:

31811

AN XY:

74226

show subpopulations

African (AFR)

AF:

0.497

AC:

20624

AN:

41480

American (AMR)

AF:

0.368

AC:

5615

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.444

AC:

1541

AN:

3472

East Asian (EAS)

AF:

0.00370

AC:

AN:

5140

South Asian (SAS)

AF:

0.295

AC:

1404

AN:

4758

European-Finnish (FIN)

AF:

0.367

AC:

3881

AN:

10564

Middle Eastern (MID)

AF:

0.558

AC:

164

AN:

294

European-Non Finnish (NFE)

AF:

0.477

AC:

32445

AN:

67956

Other (OTH)

AF:

0.451

AC:

951

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1877

3755

5632

7510

9387

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:

0.457

Hom.:

56491

Bravo

AF:

0.444

Asia WGS

AF:

0.141

AC:

489

AN:

3414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

6.0

(source)

DANN

Benign

0.77

PhyloP100

0.24

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