Variant 19-5866725-T-C 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.1001A>G(p.His334Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 148,792 control chromosomes in the GnomAD database, including 49,828 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.82 ( 49828 hom., cov: 23)

Exomes 𝑓: 0.84 ( 461590 hom. )

Failed GnomAD Quality Control

Consequence

FUT5
NM_002034.2 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.282

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=6.258451E-6).

BP6

Variant 19-5866725-T-C is Benign according to our data. Variant chr19-5866725-T-C is described in ClinVar as [Benign]. Clinvar id is 768957.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 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.1001A>G	p.His334Arg	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.1001A>G	p.His334Arg	missense_variant	2/2	1	NM_002034.2	ENSP00000466880	P1
FUT5	ENST00000252675.6 linkuse as main transcript	c.1001A>G	p.His334Arg	missense_variant	1/1			ENSP00000252675	P1

Frequencies

GnomAD3 genomes

AF:

0.816

AC:

121271

AN:

148676

Hom.:

49770

Cov.:

show subpopulations

Gnomad AFR

AF:

0.890

Gnomad AMI

AF:

0.602

Gnomad AMR

AF:

0.835

Gnomad ASJ

AF:

0.770

Gnomad EAS

AF:

0.890

Gnomad SAS

AF:

0.807

Gnomad FIN

AF:

0.711

Gnomad MID

AF:

0.812

Gnomad NFE

AF:

0.783

Gnomad OTH

AF:

0.812

GnomAD3 exomes

AF:

0.854

AC:

165814

AN:

194116

Hom.:

74904

AF XY:

0.854

AC XY:

89427

AN XY:

104666

show subpopulations

Gnomad AFR exome

AF:

0.903

Gnomad AMR exome

AF:

0.907

Gnomad ASJ exome

AF:

0.838

Gnomad EAS exome

AF:

0.917

Gnomad SAS exome

AF:

0.869

Gnomad FIN exome

AF:

0.794

Gnomad NFE exome

AF:

0.823

Gnomad OTH exome

AF:

0.850

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.841

AC:

1060679

AN:

1261624

Hom.:

461590

Cov.:

AF XY:

0.839

AC XY:

526877

AN XY:

628226

show subpopulations

Gnomad4 AFR exome

AF:

0.923

Gnomad4 AMR exome

AF:

0.899

Gnomad4 ASJ exome

AF:

0.801

Gnomad4 EAS exome

AF:

0.910

Gnomad4 SAS exome

AF:

0.839

Gnomad4 FIN exome

AF:

0.749

Gnomad4 NFE exome

AF:

0.838

Gnomad4 OTH exome

AF:

0.837

GnomAD4 genome

AF:

0.816

AC:

121392

AN:

148792

Hom.:

49828

Cov.:

AF XY:

0.814

AC XY:

58962

AN XY:

72428

show subpopulations

Gnomad4 AFR

AF:

0.891

Gnomad4 AMR

AF:

0.836

Gnomad4 ASJ

AF:

0.770

Gnomad4 EAS

AF:

0.891

Gnomad4 SAS

AF:

0.807

Gnomad4 FIN

AF:

0.711

Gnomad4 NFE

AF:

0.783

Gnomad4 OTH

AF:

0.815

Alfa

AF:

0.760

Hom.:

5085

ExAC

AF:

0.759

AC:

91508

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

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.045

BayesDel_addAF

Benign

-0.37

BayesDel_noAF

Benign

-0.77

CADD

Benign

0.76

DANN

Benign

0.17

Eigen

Benign

-0.85

Eigen_PC

Benign

-0.96

FATHMM_MKL

Benign

0.0075

LIST_S2

Benign

0.0037

T;.

MetaRNN

Benign

0.0000063

T;T

MetaSVM

Benign

-0.98

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.31

PROVEAN

Benign

1.7

N;.

REVEL

Benign

0.020

Sift

Benign

1.0

T;.

Sift4G

Benign

1.0

T;T

Vest4

0.0090

MPC

0.63

ClinPred

0.0025

GERP RS

1.3

gMVP

0.24

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