Variant 19-48703205-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_000511.6(FUT2):c.249C>T(p.Tyr83=) 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 1,612,814 control chromosomes in the GnomAD database, including 180,000 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as confers sensitivity (no stars).

Frequency

Genomes: 𝑓 0.44 ( 15745 hom., cov: 32)

Exomes 𝑓: 0.46 ( 164255 hom. )

Consequence

FUT2
NM_000511.6 synonymous

Scores

Clinical Significance

confers sensitivity no assertion criteria provided O:1

Conservation

PhyloP100: -2.90

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP7

Synonymous conserved (PhyloP=-2.9 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/exons	MANE
FUT2	NM_000511.6 linkuse as main transcript	c.249C>T	p.Tyr83=	synonymous_variant	2/2	ENST00000425340.3
LOC105447645	NR_131188.1 linkuse as main transcript	n.644G>A		non_coding_transcript_exon_variant	1/1
FUT2	NM_001097638.3 linkuse as main transcript	c.249C>T	p.Tyr83=	synonymous_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FUT2	ENST00000425340.3 linkuse as main transcript	c.249C>T	p.Tyr83=	synonymous_variant	2/2	1	NM_000511.6	P1
FUT2	ENST00000522966.2 linkuse as main transcript	c.249C>T	p.Tyr83=	synonymous_variant	2/2	2		P1

Frequencies

GnomAD3 genomes

AF:

0.442

AC:

67017

AN:

151770

Hom.:

15752

Cov.:

show subpopulations

Gnomad AFR

AF:

0.499

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:

0.368

Gnomad MID

AF:

0.582

Gnomad NFE

AF:

0.477

Gnomad OTH

AF:

0.459

GnomAD3 exomes

AF:

0.383

AC:

95841

AN:

250036

Hom.:

21390

AF XY:

0.387

AC XY:

52373

AN XY:

135276

show subpopulations

Gnomad AFR exome

AF:

0.499

Gnomad AMR exome

AF:

0.265

Gnomad ASJ exome

AF:

0.452

Gnomad EAS exome

AF:

0.00257

Gnomad SAS exome

AF:

0.314

Gnomad FIN exome

AF:

0.375

Gnomad NFE exome

AF:

0.476

Gnomad OTH exome

AF:

0.431

GnomAD4 exome

AF:

0.460

AC:

671969

AN:

1460928

Hom.:

164255

Cov.:

AF XY:

0.455

AC XY:

330703

AN XY:

726712

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 AMR exome

AF:

0.277

Gnomad4 ASJ exome

AF:

0.446

Gnomad4 EAS exome

AF:

0.00166

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:

67021

AN:

151886

Hom.:

15745

Cov.:

AF XY:

0.430

AC XY:

31857

AN XY:

74168

show subpopulations

Gnomad4 AFR

AF:

0.499

Gnomad4 AMR

AF:

0.368

Gnomad4 ASJ

AF:

0.444

Gnomad4 EAS

AF:

0.00370

Gnomad4 SAS

AF:

0.295

Gnomad4 FIN

AF:

0.368

Gnomad4 NFE

AF:

0.477

Gnomad4 OTH

AF:

0.453

Alfa

AF:

0.457

Hom.:

19050

Bravo

AF:

0.445

Asia WGS

AF:

0.142

AC:

491

AN:

3420

EpiCase

AF:

0.479

EpiControl

AF:

0.481

ClinVar

Significance: confers sensitivity

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

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

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.12

DANN

Benign

0.36

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