Genetic Variant FUT2:c.*1765T>C (chr19-48705753-T-C) – 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.*1765T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 166,720 control chromosomes in the GnomAD database, including 19,235 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 0.47 ( 17929 hom., cov: 31)

Exomes 𝑓: 0.42 ( 1306 hom. )

Consequence

FUT2
NM_000511.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.131

Publications

49 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:

MAMSTR (HGNC:26689): (MEF2 activating motif and SAP domain containing transcriptional regulator) Predicted to enable transcription coregulator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of myotube differentiation and positive regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

MAMSTR 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=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
FUT2	NM_000511.6 link	c.*1765T>C	3_prime_UTR_variant	Exon 2 of 2	ENST00000425340.3	NP_000502.4	Q10981A8K2L2
FUT2	NM_001097638.3 link	c.*1765T>C	3_prime_UTR_variant	Exon 2 of 2		NP_001091107.1	Q10981A8K2L2
MAMSTR	XM_047438640.1 link	c.*1515A>G	3_prime_UTR_variant	Exon 7 of 7		XP_047294596.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FUT2	ENST00000425340.3 link	c.*1765T>C		3_prime_UTR_variant	Exon 2 of 2	1	NM_000511.6	ENSP00000387498.2		Q10981

Frequencies

GnomAD3 genomes

AF:

0.471

AC:

71428

AN:

151698

Hom.:

17916

Cov.:

show subpopulations

Gnomad AFR

AF:

0.544

Gnomad AMI

AF:

0.355

Gnomad AMR

AF:

0.391

Gnomad ASJ

AF:

0.471

Gnomad EAS

AF:

0.00386

Gnomad SAS

AF:

0.296

Gnomad FIN

AF:

0.406

Gnomad MID

AF:

0.604

Gnomad NFE

AF:

0.503

Gnomad OTH

AF:

0.488

GnomAD4 exome

AF:

0.416

AC:

6200

AN:

14904

Hom.:

1306

Cov.:

AF XY:

0.413

AC XY:

2927

AN XY:

7080

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AF:

0.750

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.393

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.415

AC:

6084

AN:

14654

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.543

AC:

AN:

Other (OTH)

AF:

0.422

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.461

Heterozygous variant carriers

168

335

503

670

838

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.471

AC:

71476

AN:

151816

Hom.:

17929

Cov.:

AF XY:

0.458

AC XY:

33977

AN XY:

74170

show subpopulations

African (AFR)

AF:

0.544

AC:

22516

AN:

41394

American (AMR)

AF:

0.390

AC:

5948

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.471

AC:

1637

AN:

3472

East Asian (EAS)

AF:

0.00386

AC:

AN:

5176

South Asian (SAS)

AF:

0.296

AC:

1395

AN:

4716

European-Finnish (FIN)

AF:

0.406

AC:

4285

AN:

10546

Middle Eastern (MID)

AF:

0.585

AC:

172

AN:

294

European-Non Finnish (NFE)

AF:

0.503

AC:

34159

AN:

67960

Other (OTH)

AF:

0.484

AC:

1023

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1858

3716

5575

7433

9291

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

624

1248

1872

2496

3120

<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:

0.484

Hom.:

66043

Bravo

AF:

0.475

Asia WGS

AF:

0.161

AC:

556

AN:

3418

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.3

(source)

DANN

Benign

0.39

PhyloP100

-0.13

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