Variant 19-48703346-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_000511.6(FUT2):c.390C>T(p.Asn130=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 1,612,590 control chromosomes in the GnomAD database, including 171,566 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.42 ( 14954 hom., cov: 32)

Exomes 𝑓: 0.45 ( 156612 hom. )

Consequence

FUT2
NM_000511.6 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0310

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 -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.34).

BP6

Variant 19-48703346-C-T is Benign according to our data. Variant chr19-48703346-C-T is described in ClinVar as [Benign]. Clinvar id is 1288280.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.031 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
FUT2	NM_000511.6 linkuse as main transcript	c.390C>T	p.Asn130=	synonymous_variant	2/2	ENST00000425340.3
LOC105447645	NR_131188.1 linkuse as main transcript	n.503G>A		non_coding_transcript_exon_variant	1/1
FUT2	NM_001097638.3 linkuse as main transcript	c.390C>T	p.Asn130=	synonymous_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FUT2	ENST00000425340.3 linkuse as main transcript	c.390C>T	p.Asn130=	synonymous_variant	2/2	1	NM_000511.6	P1
FUT2	ENST00000522966.2 linkuse as main transcript	c.390C>T	p.Asn130=	synonymous_variant	2/2	2		P1

Frequencies

GnomAD3 genomes

AF:

0.424

AC:

64398

AN:

151762

Hom.:

14955

Cov.:

show subpopulations

Gnomad AFR

AF:

0.264

Gnomad AMI

AF:

0.493

Gnomad AMR

AF:

0.494

Gnomad ASJ

AF:

0.491

Gnomad EAS

AF:

0.850

Gnomad SAS

AF:

0.464

Gnomad FIN

AF:

0.508

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.454

Gnomad OTH

AF:

0.420

GnomAD3 exomes

AF:

0.494

AC:

123629

AN:

250030

Hom.:

33028

AF XY:

0.492

AC XY:

66679

AN XY:

135472

show subpopulations

Gnomad AFR exome

AF:

0.263

Gnomad AMR exome

AF:

0.556

Gnomad ASJ exome

AF:

0.483

Gnomad EAS exome

AF:

0.869

Gnomad SAS exome

AF:

0.473

Gnomad FIN exome

AF:

0.506

Gnomad NFE exome

AF:

0.453

Gnomad OTH exome

AF:

0.473

GnomAD4 exome

AF:

0.454

AC:

662748

AN:

1460712

Hom.:

156612

Cov.:

AF XY:

0.456

AC XY:

331037

AN XY:

726626

show subpopulations

Gnomad4 AFR exome

AF:

0.256

Gnomad4 AMR exome

AF:

0.548

Gnomad4 ASJ exome

AF:

0.486

Gnomad4 EAS exome

AF:

0.845

Gnomad4 SAS exome

AF:

0.467

Gnomad4 FIN exome

AF:

0.505

Gnomad4 NFE exome

AF:

0.438

Gnomad4 OTH exome

AF:

0.444

GnomAD4 genome

AF:

0.424

AC:

64424

AN:

151878

Hom.:

14954

Cov.:

AF XY:

0.431

AC XY:

31961

AN XY:

74196

show subpopulations

Gnomad4 AFR

AF:

0.263

Gnomad4 AMR

AF:

0.494

Gnomad4 ASJ

AF:

0.491

Gnomad4 EAS

AF:

0.850

Gnomad4 SAS

AF:

0.465

Gnomad4 FIN

AF:

0.508

Gnomad4 NFE

AF:

0.454

Gnomad4 OTH

AF:

0.420

Alfa

AF:

0.441

Hom.:

14467

Bravo

AF:

0.418

Asia WGS

AF:

0.642

AC:

2188

AN:

3416

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 29, 2020	This variant is associated with the following publications: (PMID: 22001757, 23002346) -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

FUT2-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

May 08, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.34

CADD

Benign

6.5

DANN

Benign

0.77

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