Variant 19-5866713-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002034.2(FUT5):c.1013C>T(p.Thr338Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 1,564,172 control chromosomes in the GnomAD database, including 132,463 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.36 ( 10599 hom., cov: 26)

Exomes 𝑓: 0.40 ( 121864 hom. )

Consequence

FUT5
NM_002034.2 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.247

Variant links:

Genes affected

FUT5 (HGNC:4016): (fucosyltransferase 5) Enables 3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity and 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase activity. Involved in ceramide metabolic process and oligosaccharide metabolic process. Predicted to be located in Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]

FUT5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.5839934E-4).

BP6

Variant 19-5866713-G-A is Benign according to our data. Variant chr19-5866713-G-A is described in ClinVar as [Benign]. Clinvar id is 769446.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FUT5	NM_002034.2 linkuse as main transcript	c.1013C>T	p.Thr338Met	missense_variant	2/2	ENST00000588525.1	NP_002025.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FUT5	ENST00000588525.1 linkuse as main transcript	c.1013C>T	p.Thr338Met	missense_variant	2/2	1	NM_002034.2	ENSP00000466880	P1
FUT5	ENST00000252675.6 linkuse as main transcript	c.1013C>T	p.Thr338Met	missense_variant	1/1			ENSP00000252675	P1

Frequencies

GnomAD3 genomes

AF:

0.363

AC:

54492

AN:

149990

Hom.:

10589

Cov.:

show subpopulations

Gnomad AFR

AF:

0.239

Gnomad AMI

AF:

0.426

Gnomad AMR

AF:

0.485

Gnomad ASJ

AF:

0.358

Gnomad EAS

AF:

0.558

Gnomad SAS

AF:

0.390

Gnomad FIN

AF:

0.377

Gnomad MID

AF:

0.385

Gnomad NFE

AF:

0.392

Gnomad OTH

AF:

0.341

GnomAD3 exomes

AF:

0.418

AC:

99842

AN:

239032

Hom.:

22622

AF XY:

0.411

AC XY:

53445

AN XY:

130074

show subpopulations

Gnomad AFR exome

AF:

0.244

Gnomad AMR exome

AF:

0.590

Gnomad ASJ exome

AF:

0.354

Gnomad EAS exome

AF:

0.539

Gnomad SAS exome

AF:

0.391

Gnomad FIN exome

AF:

0.379

Gnomad NFE exome

AF:

0.389

Gnomad OTH exome

AF:

0.408

GnomAD4 exome

AF:

0.402

AC:

567896

AN:

1414068

Hom.:

121864

Cov.:

AF XY:

0.400

AC XY:

281745

AN XY:

704058

show subpopulations

Gnomad4 AFR exome

AF:

0.240

Gnomad4 AMR exome

AF:

0.580

Gnomad4 ASJ exome

AF:

0.357

Gnomad4 EAS exome

AF:

0.589

Gnomad4 SAS exome

AF:

0.395

Gnomad4 FIN exome

AF:

0.383

Gnomad4 NFE exome

AF:

0.395

Gnomad4 OTH exome

AF:

0.399

GnomAD4 genome

AF:

0.363

AC:

54537

AN:

150104

Hom.:

10599

Cov.:

AF XY:

0.368

AC XY:

26901

AN XY:

73182

show subpopulations

Gnomad4 AFR

AF:

0.239

Gnomad4 AMR

AF:

0.485

Gnomad4 ASJ

AF:

0.358

Gnomad4 EAS

AF:

0.559

Gnomad4 SAS

AF:

0.390

Gnomad4 FIN

AF:

0.377

Gnomad4 NFE

AF:

0.392

Gnomad4 OTH

AF:

0.344

Alfa

AF:

0.375

Hom.:

1795

Bravo

AF:

0.369

ESP6500AA

AF:

0.241

AC:

1061

ESP6500EA

AF:

0.370

AC:

3181

ExAC

AF:

0.405

AC:

48947

Asia WGS

AF:

0.445

AC:

1543

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Nov 30, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.080

BayesDel_addAF

Benign

-0.26

BayesDel_noAF

Benign

-0.62

CADD

Benign

DANN

Uncertain

0.98

Eigen

Benign

-0.39

Eigen_PC

Benign

-0.54

FATHMM_MKL

Benign

0.13

LIST_S2

Benign

0.66

T;.

MetaRNN

Benign

0.00016

T;T

MetaSVM

Benign

-0.92

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.34

PROVEAN

Benign

-1.8

N;.

REVEL

Benign

0.056

Sift

Benign

0.044

D;.

Sift4G

Uncertain

0.055

T;T

Vest4

0.054

MPC

0.70

ClinPred

0.0044

GERP RS

0.91

gMVP

0.25

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