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GeneBe

19-48703417-G-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4BP6_ModerateBA1

The NM_000511.6(FUT2):c.461G>A(p.Trp154Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.458 in 1,612,604 control chromosomes in the GnomAD database, including 179,977 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.44 ( 15740 hom., cov: 32)
Exomes 𝑓: 0.46 ( 164237 hom. )

Consequence

FUT2
NM_000511.6 stop_gained

Scores

3
3
1

Clinical Significance

Benign criteria provided, single submitter B:2O:2

Conservation

PhyloP100: 4.26
Variant links:
Genes affected
FUT2 (HGNC:4013): (fucosyltransferase 2 (H blood group)) This gene is one of two encoding the galactoside 2-L-fucosyltransferase enzyme. The encoded protein is important for the final step in the soluble ABO blood group antigen synthesis pathway. It is also involved in cell-cell interaction, cell surface expression, and cell proliferation. Mutations in this gene are a cause of the H-Bombay blood group where red blood cells lack the H antigen. [provided by RefSeq, May 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

PM4
?
    PM4 - Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants
Stoplost variant in NM_000511.6 Downstream stopcodon found after 383 codons.
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 19-48703417-G-A is Benign according to our data. Variant chr19-48703417-G-A is described in ClinVar as [Benign]. Clinvar id is 12945.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FUT2NM_000511.6 linkuse as main transcriptc.461G>A p.Trp154Ter stop_gained 2/2 ENST00000425340.3
LOC105447645NR_131188.1 linkuse as main transcriptn.432C>T non_coding_transcript_exon_variant 1/1
FUT2NM_001097638.3 linkuse as main transcriptc.461G>A p.Trp154Ter stop_gained 2/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FUT2ENST00000425340.3 linkuse as main transcriptc.461G>A p.Trp154Ter stop_gained 2/21 NM_000511.6 P1
FUT2ENST00000522966.2 linkuse as main transcriptc.461G>A p.Trp154Ter stop_gained 2/22 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.441
AC:
66996
AN:
151762
Hom.:
15747
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.499
Gnomad AMI
AF:
0.351
Gnomad AMR
AF:
0.369
Gnomad ASJ
AF:
0.444
Gnomad EAS
AF:
0.00386
Gnomad SAS
AF:
0.296
Gnomad FIN
AF:
0.368
Gnomad MID
AF:
0.582
Gnomad NFE
AF:
0.478
Gnomad OTH
AF:
0.458
GnomAD3 exomes
AF:
0.383
AC:
95772
AN:
250156
Hom.:
21385
AF XY:
0.387
AC XY:
52463
AN XY:
135516
show subpopulations
Gnomad AFR exome
AF:
0.498
Gnomad AMR exome
AF:
0.265
Gnomad ASJ exome
AF:
0.451
Gnomad EAS exome
AF:
0.00224
Gnomad SAS exome
AF:
0.315
Gnomad FIN exome
AF:
0.374
Gnomad NFE exome
AF:
0.476
Gnomad OTH exome
AF:
0.431
GnomAD4 exome
AF:
0.460
AC:
671929
AN:
1460728
Hom.:
164237
Cov.:
75
AF XY:
0.455
AC XY:
330704
AN XY:
726622
show subpopulations
Gnomad4 AFR exome
AF:
0.500
Gnomad4 AMR exome
AF:
0.277
Gnomad4 ASJ exome
AF:
0.446
Gnomad4 EAS exome
AF:
0.00159
Gnomad4 SAS exome
AF:
0.320
Gnomad4 FIN exome
AF:
0.376
Gnomad4 NFE exome
AF:
0.497
Gnomad4 OTH exome
AF:
0.463
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.441
AC:
67000
AN:
151876
Hom.:
15740
Cov.:
32
AF XY:
0.429
AC XY:
31842
AN XY:
74210
show subpopulations
Gnomad4 AFR
AF:
0.499
Gnomad4 AMR
AF:
0.368
Gnomad4 ASJ
AF:
0.444
Gnomad4 EAS
AF:
0.00387
Gnomad4 SAS
AF:
0.295
Gnomad4 FIN
AF:
0.368
Gnomad4 NFE
AF:
0.478
Gnomad4 OTH
AF:
0.452
Alfa
AF:
0.471
Hom.:
16358
Bravo
AF:
0.445
TwinsUK
AF:
0.494
AC:
1830
ALSPAC
AF:
0.499
AC:
1924
ESP6500AA
AF:
0.496
AC:
2186
ESP6500EA
AF:
0.492
AC:
4231
ExAC
?
    Exome Aggregation Consortium database
AF:
0.389
AC:
47143
Asia WGS
AF:
0.141
AC:
490
AN:
3414
EpiCase
AF:
0.480
EpiControl
AF:
0.480

ClinVar

Significance: Benign
Submissions summary: Benign:2Other:2
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

SECRETOR/NONSECRETOR POLYMORPHISM Benign:1
Benign, no assertion criteria providedliterature onlyOMIMOct 01, 2008- -
Bombay phenotype;C2674252:Vitamin b12 plasma level quantitative trait locus 1 Benign:1
Benign, criteria provided, single submitterclinical testingFulgent Genetics, Fulgent GeneticsAug 12, 2021- -
Familial Otitis Media Other:1
confers sensitivity, no assertion criteria providedresearchUniversity of Washington Center for Mendelian Genomics, University of Washington-- -
Vitamin b12 plasma level quantitative trait locus 1 Other:1
association, no assertion criteria providedliterature onlyOMIMOct 01, 2008- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
0.16
D
BayesDel_noAF
Pathogenic
0.60
Cadd
Pathogenic
46
Dann
Uncertain
1.0
Eigen
Pathogenic
0.81
Eigen_PC
Pathogenic
0.67
FATHMM_MKL
Uncertain
0.89
D
MutationTaster
Benign
6.4e-17
P;P
Vest4
0.70, 0.53
GERP RS
4.8

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.

Other links and lift over

dbSNP: rs601338; hg19: chr19-49206674; COSMIC: COSV67178879; API