Variant 19-48751247-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_001384359.1(FUT1):c.35C>T(p.Ala12Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0343 in 1,614,056 control chromosomes in the GnomAD database, including 3,804 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.032 ( 311 hom., cov: 33)

Exomes 𝑓: 0.035 ( 3493 hom. )

Consequence

FUT1
NM_001384359.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0240

Variant links:

Genes affected

FUT1 (HGNC:4012): (fucosyltransferase 1 (H blood group)) This gene encodes a Golgi stack membrane protein that is involved in the creation of a precursor of the H antigen, which is required for the final step in the synthesis of soluble A and B antigens. This is one of two genes encoding the galactoside 2-L-fucosyltransferase enzyme. Mutations in this gene are a cause of the H-Bombay blood group. [provided by RefSeq, Aug 2016]

FUT1 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 (MetaRNN=0.0031044483).

BP6

Variant 19-48751247-G-A is Benign according to our data. Variant chr19-48751247-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3056653.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
FUT1	NM_001384359.1 linkuse as main transcript	c.35C>T	p.Ala12Val	missense_variant	2/2	ENST00000645652.2
FUT1	NM_000148.4 linkuse as main transcript	c.35C>T	p.Ala12Val	missense_variant	4/4
FUT1	NM_001329877.1 linkuse as main transcript	c.35C>T	p.Ala12Val	missense_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FUT1	ENST00000645652.2 linkuse as main transcript	c.35C>T	p.Ala12Val	missense_variant	2/2		NM_001384359.1	P1

Frequencies

GnomAD3 genomes

AF:

0.0317

AC:

4829

AN:

152170

Hom.:

313

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00413

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0361

Gnomad ASJ

AF:

0.0308

Gnomad EAS

AF:

0.291

Gnomad SAS

AF:

0.114

Gnomad FIN

AF:

0.0447

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0205

Gnomad OTH

AF:

0.0272

GnomAD3 exomes

AF:

0.0590

AC:

14801

AN:

250760

Hom.:

1119

AF XY:

0.0587

AC XY:

7968

AN XY:

135658

show subpopulations

Gnomad AFR exome

AF:

0.00315

Gnomad AMR exome

AF:

0.0805

Gnomad ASJ exome

AF:

0.0279

Gnomad EAS exome

AF:

0.282

Gnomad SAS exome

AF:

0.101

Gnomad FIN exome

AF:

0.0460

Gnomad NFE exome

AF:

0.0187

Gnomad OTH exome

AF:

0.0486

GnomAD4 exome

AF:

0.0346

AC:

50600

AN:

1461768

Hom.:

3493

Cov.:

AF XY:

0.0363

AC XY:

26409

AN XY:

727170

show subpopulations

Gnomad4 AFR exome

AF:

0.00335

Gnomad4 AMR exome

AF:

0.0739

Gnomad4 ASJ exome

AF:

0.0283

Gnomad4 EAS exome

AF:

0.344

Gnomad4 SAS exome

AF:

0.0996

Gnomad4 FIN exome

AF:

0.0434

Gnomad4 NFE exome

AF:

0.0173

Gnomad4 OTH exome

AF:

0.0398

GnomAD4 genome

AF:

0.0317

AC:

4821

AN:

152288

Hom.:

311

Cov.:

AF XY:

0.0358

AC XY:

2669

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.00411

Gnomad4 AMR

AF:

0.0360

Gnomad4 ASJ

AF:

0.0308

Gnomad4 EAS

AF:

0.291

Gnomad4 SAS

AF:

0.113

Gnomad4 FIN

AF:

0.0447

Gnomad4 NFE

AF:

0.0205

Gnomad4 OTH

AF:

0.0284

Alfa

AF:

0.0225

Hom.:

117

Bravo

AF:

0.0302

TwinsUK

AF:

0.0154

AC:

ALSPAC

AF:

0.0187

AC:

ESP6500AA

AF:

0.00363

AC:

ESP6500EA

AF:

0.0207

AC:

178

ExAC

AF:

0.0572

AC:

6946

Asia WGS

AF:

0.182

AC:

630

AN:

3478

EpiCase

AF:

0.0192

EpiControl

AF:

0.0208

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

FUT1-related disorder

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 25, 2020

This variant is classified as likely 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

AlphaMissense

Benign

0.090

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.57

CADD

Benign

DANN

Benign

0.97

DEOGEN2

Benign

0.18

T;T

Eigen

Benign

-0.83

Eigen_PC

Benign

-0.76

FATHMM_MKL

Benign

0.54

LIST_S2

Benign

0.61

.;T

MetaRNN

Benign

0.0031

T;T

MetaSVM

Benign

-0.99

MutationAssessor

Benign

1.7

L;L

MutationTaster

Benign

0.94

PrimateAI

Benign

0.27

PROVEAN

Benign

-0.14

.;N

REVEL

Benign

0.029

Sift

Benign

0.064

.;T

Sift4G

Benign

1.0

.;T

Polyphen

0.10

B;B

Vest4

0.023

MPC

0.43

ClinPred

0.0051

GERP RS

-1.3

Varity_R

0.045

gMVP

0.44

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