Variant 19-48703374-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_000511.6(FUT2):c.418A>T(p.Ile140Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 1,613,090 control chromosomes in the GnomAD database, including 4,633 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.017 ( 535 hom., cov: 32)

Exomes 𝑓: 0.014 ( 4098 hom. )

Consequence

FUT2
NM_000511.6 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:2O:1

Conservation

PhyloP100: 2.16

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 made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004746765).

BP6

Variant 19-48703374-A-T is Benign according to our data. Variant chr19-48703374-A-T is described in ClinVar as [Benign]. Clinvar id is 12946.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-48703374-A-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
FUT2	NM_000511.6 linkuse as main transcript	c.418A>T	p.Ile140Phe	missense_variant	2/2	ENST00000425340.3
LOC105447645	NR_131188.1 linkuse as main transcript	n.475T>A		non_coding_transcript_exon_variant	1/1
FUT2	NM_001097638.3 linkuse as main transcript	c.418A>T	p.Ile140Phe	missense_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FUT2	ENST00000425340.3 linkuse as main transcript	c.418A>T	p.Ile140Phe	missense_variant	2/2	1	NM_000511.6	P1
FUT2	ENST00000522966.2 linkuse as main transcript	c.418A>T	p.Ile140Phe	missense_variant	2/2	2		P1

Frequencies

GnomAD3 genomes

AF:

0.0168

AC:

2562

AN:

152064

Hom.:

535

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00109

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00367

Gnomad ASJ

AF:

0.000865

Gnomad EAS

AF:

0.446

Gnomad SAS

AF:

0.0189

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000323

Gnomad OTH

AF:

0.0177

GnomAD3 exomes

AF:

0.0364

AC:

9127

AN:

250590

Hom.:

2067

AF XY:

0.0338

AC XY:

4590

AN XY:

135668

show subpopulations

Gnomad AFR exome

AF:

0.00118

Gnomad AMR exome

AF:

0.000838

Gnomad ASJ exome

AF:

0.000894

Gnomad EAS exome

AF:

0.472

Gnomad SAS exome

AF:

0.00855

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000309

Gnomad OTH exome

AF:

0.0183

GnomAD4 exome

AF:

0.0138

AC:

20210

AN:

1460908

Hom.:

4098

Cov.:

AF XY:

0.0135

AC XY:

9825

AN XY:

726718

show subpopulations

Gnomad4 AFR exome

AF:

0.000806

Gnomad4 AMR exome

AF:

0.000827

Gnomad4 ASJ exome

AF:

0.00122

Gnomad4 EAS exome

AF:

0.440

Gnomad4 SAS exome

AF:

0.0101

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000196

Gnomad4 OTH exome

AF:

0.0254

GnomAD4 genome

AF:

0.0168

AC:

2558

AN:

152182

Hom.:

535

Cov.:

AF XY:

0.0192

AC XY:

1432

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.00108

Gnomad4 AMR

AF:

0.00366

Gnomad4 ASJ

AF:

0.000865

Gnomad4 EAS

AF:

0.446

Gnomad4 SAS

AF:

0.0190

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000323

Gnomad4 OTH

AF:

0.0189

Alfa

AF:

0.0150

Hom.:

375

Bravo

AF:

0.0198

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.000778

AC:

ESP6500AA

AF:

0.00159

AC:

ESP6500EA

AF:

0.000233

AC:

ExAC

AF:

0.0349

AC:

4232

Asia WGS

AF:

0.164

AC:

558

AN:

3412

EpiCase

AF:

0.000600

EpiControl

AF:

0.000415

ClinVar

Significance: Benign

Submissions summary: Benign:2Other:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

SECRETOR/NONSECRETOR POLYMORPHISM, JAPANESE TYPE

Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Apr 19, 1996

- -

Familial Otitis Media

Other:1

confers sensitivity, no assertion criteria provided

research

University of Washington Center for Mendelian Genomics, University of Washington

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.47

BayesDel_addAF

Benign

-0.11

BayesDel_noAF

Pathogenic

0.21

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.11

.;T;T

Eigen

Uncertain

0.36

Eigen_PC

Uncertain

0.24

FATHMM_MKL

Benign

0.72

LIST_S2

Benign

0.68

.;.;T

MetaRNN

Benign

0.0047

T;T;T

MetaSVM

Benign

-1.6

MutationAssessor

Pathogenic

2.9

.;M;M

MutationTaster

Benign

0.0073

P;P

PrimateAI

Benign

0.48

PROVEAN

Uncertain

-3.0

D;D;D

REVEL

Pathogenic

0.78

Sift

Uncertain

0.0030

D;D;D

Sift4G

Uncertain

0.0050

D;T;T

Polyphen

0.98

.;D;D

Vest4

0.25, 0.17

MPC

0.89

ClinPred

0.043

GERP RS

3.8

Varity_R

0.44

gMVP

0.56

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