Variant rs3762001 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032020.5(FUCA2):c.1111C>T(p.His371Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 1,612,406 control chromosomes in the GnomAD database, including 37,759 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.20 ( 3150 hom., cov: 31)

Exomes 𝑓: 0.21 ( 34609 hom. )

Consequence

FUCA2
NM_032020.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.18

Variant links:

Genes affected

FUCA2 (HGNC:4008): (alpha-L-fucosidase 2) This gene encodes a plasma alpha-L-fucosidase, which represents 10-20% of the total cellular fucosidase activity. The protein is a member of the glycosyl hydrolase 29 family, and catalyzes the hydrolysis of the alpha-1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the carbohydrate moieties of glycoproteins. This enzyme is essential for Helicobacter pylori adhesion to human gastric cancer cells. [provided by RefSeq, Aug 2010]

FUCA2 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.01053381).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FUCA2	NM_032020.5 linkuse as main transcript	c.1111C>T	p.His371Tyr	missense_variant	5/7	ENST00000002165.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FUCA2	ENST00000002165.11 linkuse as main transcript	c.1111C>T	p.His371Tyr	missense_variant	5/7	1	NM_032020.5	P1	Q9BTY2-1
	ENST00000589563.5 linkuse as main transcript	n.502-3365G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.198

AC:

30086

AN:

151788

Hom.:

3153

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.128

Gnomad AMR

AF:

0.154

Gnomad ASJ

AF:

0.346

Gnomad EAS

AF:

0.180

Gnomad SAS

AF:

0.174

Gnomad FIN

AF:

0.296

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.220

Gnomad OTH

AF:

0.188

GnomAD3 exomes

AF:

0.207

AC:

51901

AN:

251222

Hom.:

5770

AF XY:

0.209

AC XY:

28434

AN XY:

135774

show subpopulations

Gnomad AFR exome

AF:

0.145

Gnomad AMR exome

AF:

0.131

Gnomad ASJ exome

AF:

0.330

Gnomad EAS exome

AF:

0.182

Gnomad SAS exome

AF:

0.187

Gnomad FIN exome

AF:

0.284

Gnomad NFE exome

AF:

0.222

Gnomad OTH exome

AF:

0.205

GnomAD4 exome

AF:

0.215

AC:

313796

AN:

1460500

Hom.:

34609

Cov.:

AF XY:

0.215

AC XY:

156320

AN XY:

726552

show subpopulations

Gnomad4 AFR exome

AF:

0.146

Gnomad4 AMR exome

AF:

0.133

Gnomad4 ASJ exome

AF:

0.332

Gnomad4 EAS exome

AF:

0.205

Gnomad4 SAS exome

AF:

0.187

Gnomad4 FIN exome

AF:

0.278

Gnomad4 NFE exome

AF:

0.217

Gnomad4 OTH exome

AF:

0.211

GnomAD4 genome

AF:

0.198

AC:

30085

AN:

151906

Hom.:

3150

Cov.:

AF XY:

0.199

AC XY:

14783

AN XY:

74232

show subpopulations

Gnomad4 AFR

AF:

0.148

Gnomad4 AMR

AF:

0.154

Gnomad4 ASJ

AF:

0.346

Gnomad4 EAS

AF:

0.180

Gnomad4 SAS

AF:

0.174

Gnomad4 FIN

AF:

0.296

Gnomad4 NFE

AF:

0.220

Gnomad4 OTH

AF:

0.188

Alfa

AF:

0.215

Hom.:

8346

Bravo

AF:

0.186

TwinsUK

AF:

0.222

AC:

823

ALSPAC

AF:

0.219

AC:

845

ESP6500AA

AF:

0.153

AC:

676

ESP6500EA

AF:

0.225

AC:

1934

ExAC

AF:

0.206

AC:

25051

Asia WGS

AF:

0.174

AC:

604

AN:

3478

EpiCase

AF:

0.219

EpiControl

AF:

0.221

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.087

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.55

Cadd

Benign

5.4

Dann

Benign

0.90

DEOGEN2

Benign

0.078

T;T

Eigen

Benign

-0.71

Eigen_PC

Benign

-0.68

FATHMM_MKL

Benign

0.28

LIST_S2

Benign

0.70

T;T

MetaRNN

Benign

0.011

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.7

L;.

MutationTaster

Benign

1.0

P;P;P

PrimateAI

Benign

0.28

PROVEAN

Benign

-1.1

N;N

REVEL

Benign

0.095

Sift

Benign

0.14

T;T

Sift4G

Benign

0.90

T;T

Polyphen

0.0

B;B

Vest4

0.073

MPC

0.21

ClinPred

0.0023

GERP RS

-1.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.079

gMVP

0.48

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over