Variant 19-5844108-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001382749.2(FUT3):c.732C>T(p.Tyr244=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00122 in 1,611,856 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0068 ( 8 hom., cov: 31)

Exomes 𝑓: 0.00064 ( 7 hom. )

Consequence

FUT3
NM_001382749.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.45

Variant links:

Genes affected

FUT3 (HGNC:4014): (fucosyltransferase 3 (Lewis blood group)) The Lewis histo-blood group system comprises a set of fucosylated glycosphingolipids that are synthesized by exocrine epithelial cells and circulate in body fluids. The glycosphingolipids function in embryogenesis, tissue differentiation, tumor metastasis, inflammation, and bacterial adhesion. They are secondarily absorbed to red blood cells giving rise to their Lewis phenotype. This gene is a member of the fucosyltransferase family, which catalyzes the addition of fucose to precursor polysaccharides in the last step of Lewis antigen biosynthesis. It encodes an enzyme with alpha(1,3)-fucosyltransferase and alpha(1,4)-fucosyltransferase activities. Mutations in this gene are responsible for the majority of Lewis antigen-negative phenotypes. Differences in the expression of this gene are associated with host susceptibility to viral infection. [provided by RefSeq, Aug 2020]

FUT3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP6

Variant 19-5844108-G-A is Benign according to our data. Variant chr19-5844108-G-A is described in ClinVar as [Benign]. Clinvar id is 718641.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=2.45 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00682 (1036/151852) while in subpopulation AFR AF= 0.0204 (841/41230). AF 95% confidence interval is 0.0193. There are 8 homozygotes in gnomad4. There are 475 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High AC in GnomAd4 at 1036 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FUT3	NM_001097639.3 linkuse as main transcript	c.732C>T	p.Tyr244=	synonymous_variant	3/3	ENST00000709635.1
FUT3	NM_001382749.2 linkuse as main transcript	c.732C>T	p.Tyr244=	synonymous_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	Appris
FUT3	ENST00000303225.12 linkuse as main transcript	c.732C>T	p.Tyr244=	synonymous_variant	3/3	1	P1
FUT3	ENST00000458379.7 linkuse as main transcript	c.732C>T	p.Tyr244=	synonymous_variant	2/2	1	P1
FUT3	ENST00000589620.6 linkuse as main transcript	c.732C>T	p.Tyr244=	synonymous_variant	3/3	1	P1
FUT3	ENST00000589918.5 linkuse as main transcript	c.732C>T	p.Tyr244=	synonymous_variant	3/3	1	P1

Frequencies

GnomAD3 genomes

AF:

0.00679

AC:

1030

AN:

151738

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0203

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00445

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00271

Gnomad SAS

AF:

0.00249

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00121

Gnomad OTH

AF:

0.00720

GnomAD3 exomes

AF:

0.000899

AC:

226

AN:

251334

Hom.:

AF XY:

0.000810

AC XY:

110

AN XY:

135846

show subpopulations

Gnomad AFR exome

AF:

0.00746

Gnomad AMR exome

AF:

0.000810

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00103

Gnomad SAS exome

AF:

0.000555

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000325

Gnomad OTH exome

AF:

0.000652

GnomAD4 exome

AF:

0.000639

AC:

933

AN:

1460004

Hom.:

Cov.:

AF XY:

0.000633

AC XY:

460

AN XY:

726366

show subpopulations

Gnomad4 AFR exome

AF:

0.00877

Gnomad4 AMR exome

AF:

0.00123

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00181

Gnomad4 SAS exome

AF:

0.00132

Gnomad4 FIN exome

AF:

0.0000374

Gnomad4 NFE exome

AF:

0.000292

Gnomad4 OTH exome

AF:

0.00123

GnomAD4 genome

AF:

0.00682

AC:

1036

AN:

151852

Hom.:

Cov.:

AF XY:

0.00640

AC XY:

475

AN XY:

74232

show subpopulations

Gnomad4 AFR

AF:

0.0204

Gnomad4 AMR

AF:

0.00445

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00271

Gnomad4 SAS

AF:

0.00249

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00121

Gnomad4 OTH

AF:

0.00712

Alfa

AF:

0.00363

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jun 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

1.6

DANN

Benign

0.63

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