Variant chr19-48703417-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_000511.6(FUT2):c.461G>A(p.Trp154Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.458 in 1,612,604 control chromosomes in the GnomAD database, including 179,977 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.44 ( 15740 hom., cov: 32)

Exomes 𝑓: 0.46 ( 164237 hom. )

Consequence

FUT2
NM_000511.6 stop_gained

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3O:2

Conservation

PhyloP100: 4.26

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 made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 19-48703417-G-A is Benign according to our data. Variant chr19-48703417-G-A is described in ClinVar as [Benign]. Clinvar id is 12945.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

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/exons	MANE
FUT2	NM_000511.6 linkuse as main transcript	c.461G>A	p.Trp154Ter	stop_gained	2/2	ENST00000425340.3
LOC105447645	NR_131188.1 linkuse as main transcript	n.432C>T		non_coding_transcript_exon_variant	1/1
FUT2	NM_001097638.3 linkuse as main transcript	c.461G>A	p.Trp154Ter	stop_gained	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FUT2	ENST00000425340.3 linkuse as main transcript	c.461G>A	p.Trp154Ter	stop_gained	2/2	1	NM_000511.6	P1
FUT2	ENST00000522966.2 linkuse as main transcript	c.461G>A	p.Trp154Ter	stop_gained	2/2	2		P1

Frequencies

GnomAD3 genomes

AF:

0.441

AC:

66996

AN:

151762

Hom.:

15747

Cov.:

show subpopulations

Gnomad AFR

AF:

0.499

Gnomad AMI

AF:

0.351

Gnomad AMR

AF:

0.369

Gnomad ASJ

AF:

0.444

Gnomad EAS

AF:

0.00386

Gnomad SAS

AF:

0.296

Gnomad FIN

AF:

0.368

Gnomad MID

AF:

0.582

Gnomad NFE

AF:

0.478

Gnomad OTH

AF:

0.458

GnomAD3 exomes

AF:

0.383

AC:

95772

AN:

250156

Hom.:

21385

AF XY:

0.387

AC XY:

52463

AN XY:

135516

show subpopulations

Gnomad AFR exome

AF:

0.498

Gnomad AMR exome

AF:

0.265

Gnomad ASJ exome

AF:

0.451

Gnomad EAS exome

AF:

0.00224

Gnomad SAS exome

AF:

0.315

Gnomad FIN exome

AF:

0.374

Gnomad NFE exome

AF:

0.476

Gnomad OTH exome

AF:

0.431

GnomAD4 exome

AF:

0.460

AC:

671929

AN:

1460728

Hom.:

164237

Cov.:

AF XY:

0.455

AC XY:

330704

AN XY:

726622

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 AMR exome

AF:

0.277

Gnomad4 ASJ exome

AF:

0.446

Gnomad4 EAS exome

AF:

0.00159

Gnomad4 SAS exome

AF:

0.320

Gnomad4 FIN exome

AF:

0.376

Gnomad4 NFE exome

AF:

0.497

Gnomad4 OTH exome

AF:

0.463

GnomAD4 genome

AF:

0.441

AC:

67000

AN:

151876

Hom.:

15740

Cov.:

AF XY:

0.429

AC XY:

31842

AN XY:

74210

show subpopulations

Gnomad4 AFR

AF:

0.499

Gnomad4 AMR

AF:

0.368

Gnomad4 ASJ

AF:

0.444

Gnomad4 EAS

AF:

0.00387

Gnomad4 SAS

AF:

0.295

Gnomad4 FIN

AF:

0.368

Gnomad4 NFE

AF:

0.478

Gnomad4 OTH

AF:

0.452

Alfa

AF:

0.471

Hom.:

16358

Bravo

AF:

0.445

TwinsUK

AF:

0.494

AC:

1830

ALSPAC

AF:

0.499

AC:

1924

ESP6500AA

AF:

0.496

AC:

2186

ESP6500EA

AF:

0.492

AC:

4231

ExAC

AF:

0.389

AC:

47143

Asia WGS

AF:

0.141

AC:

490

AN:

3414

EpiCase

AF:

0.480

EpiControl

AF:

0.480

ClinVar

Significance: Benign

Submissions summary: Benign:3Other:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

SECRETOR/NONSECRETOR POLYMORPHISM

Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Oct 01, 2008

- -

Bombay phenotype;C2674252:Vitamin b12 plasma level quantitative trait locus 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Aug 12, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Familial Otitis Media

Other:1

confers sensitivity, no assertion criteria provided

research

University of Washington Center for Mendelian Genomics, University of Washington

- -

Vitamin b12 plasma level quantitative trait locus 1

Other:1

association, no assertion criteria provided

literature only

OMIM

Oct 01, 2008

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Uncertain

0.16

BayesDel_noAF

Pathogenic

0.60

CADD

Pathogenic

DANN

Uncertain

1.0

Eigen

Pathogenic

0.81

Eigen_PC

Pathogenic

0.67

FATHMM_MKL

Uncertain

0.89

MutationTaster

Benign

6.4e-17

P;P

Vest4

0.70, 0.53

GERP RS

4.8

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