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GeneBe

19-48703364-A-G

Variant summary

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

The NM_000511.6(FUT2):c.408A>G(p.Glu136=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00169 in 1,611,408 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0060 ( 19 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 10 hom. )

Consequence

FUT2
NM_000511.6 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.44
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 -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 19-48703364-A-G is Benign according to our data. Variant chr19-48703364-A-G is described in ClinVar as [Benign]. Clinvar id is 714890.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.44 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00602 (916/152146) while in subpopulation AFR AF= 0.0194 (806/41560). AF 95% confidence interval is 0.0183. There are 19 homozygotes in gnomad4. There are 452 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 17 BG gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FUT2NM_000511.6 linkuse as main transcriptc.408A>G p.Glu136= synonymous_variant 2/2 ENST00000425340.3
LOC105447645NR_131188.1 linkuse as main transcriptn.485T>C non_coding_transcript_exon_variant 1/1
FUT2NM_001097638.3 linkuse as main transcriptc.408A>G p.Glu136= synonymous_variant 2/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FUT2ENST00000425340.3 linkuse as main transcriptc.408A>G p.Glu136= synonymous_variant 2/21 NM_000511.6 P1
FUT2ENST00000522966.2 linkuse as main transcriptc.408A>G p.Glu136= synonymous_variant 2/22 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00597
AC:
907
AN:
152030
Hom.:
17
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0194
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00177
Gnomad ASJ
AF:
0.00317
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000420
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000868
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.00185
AC:
462
AN:
250230
Hom.:
5
AF XY:
0.00159
AC XY:
216
AN XY:
135550
show subpopulations
Gnomad AFR exome
AF:
0.0191
Gnomad AMR exome
AF:
0.000781
Gnomad ASJ exome
AF:
0.00209
Gnomad EAS exome
AF:
0.000218
Gnomad SAS exome
AF:
0.000362
Gnomad FIN exome
AF:
0.0000462
Gnomad NFE exome
AF:
0.000753
Gnomad OTH exome
AF:
0.000817
GnomAD4 exome
AF:
0.00124
AC:
1807
AN:
1459262
Hom.:
10
Cov.:
77
AF XY:
0.00119
AC XY:
861
AN XY:
725960
show subpopulations
Gnomad4 AFR exome
AF:
0.0200
Gnomad4 AMR exome
AF:
0.000962
Gnomad4 ASJ exome
AF:
0.00207
Gnomad4 EAS exome
AF:
0.000403
Gnomad4 SAS exome
AF:
0.000349
Gnomad4 FIN exome
AF:
0.0000190
Gnomad4 NFE exome
AF:
0.000773
Gnomad4 OTH exome
AF:
0.00212
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00602
AC:
916
AN:
152146
Hom.:
19
Cov.:
32
AF XY:
0.00608
AC XY:
452
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.0194
Gnomad4 AMR
AF:
0.00177
Gnomad4 ASJ
AF:
0.00317
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000421
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000868
Gnomad4 OTH
AF:
0.00521
Alfa
AF:
0.00404
Hom.:
1
Bravo
AF:
0.00705
Asia WGS
AF:
0.0160
AC:
55
AN:
3416
EpiCase
AF:
0.000765
EpiControl
AF:
0.000593

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 submitterclinical testingInvitaeAug 17, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
Cadd
Benign
0.33
Dann
Benign
0.46

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: rs1800026; hg19: chr19-49206621; API