rs3732443

Variant summary

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

The NM_001080393.2(GXYLT2):​c.977-114G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0572 in 797,204 control chromosomes in the GnomAD database, including 3,421 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.050 ( 535 hom., cov: 33)
Exomes 𝑓: 0.059 ( 2886 hom. )

Consequence

GXYLT2
NM_001080393.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.48
Variant links:
Genes affected
GXYLT2 (HGNC:33383): (glucoside xylosyltransferase 2) The protein encoded by this gene is a xylosyltransferase that elongates O-linked glucose bound to epidermal growth factor (EGF) repeats. The encoded protein catalyzes the addition of xylose to the O-glucose-modified residues of EGF repeats of Notch proteins. [provided by RefSeq, Sep 2016]

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 (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GXYLT2NM_001080393.2 linkuse as main transcriptc.977-114G>C intron_variant ENST00000389617.9 NP_001073862.1 A0PJZ3
GXYLT2NR_138564.2 linkuse as main transcriptn.1160-114G>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GXYLT2ENST00000389617.9 linkuse as main transcriptc.977-114G>C intron_variant 5 NM_001080393.2 ENSP00000374268.4 A0PJZ3
GXYLT2ENST00000491839.1 linkuse as main transcriptc.260-114G>C intron_variant 3 ENSP00000420426.1 C9JND4

Frequencies

GnomAD3 genomes
AF:
0.0503
AC:
7653
AN:
152090
Hom.:
533
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0110
Gnomad AMI
AF:
0.00658
Gnomad AMR
AF:
0.119
Gnomad ASJ
AF:
0.0467
Gnomad EAS
AF:
0.345
Gnomad SAS
AF:
0.0946
Gnomad FIN
AF:
0.0518
Gnomad MID
AF:
0.0316
Gnomad NFE
AF:
0.0336
Gnomad OTH
AF:
0.0617
GnomAD4 exome
AF:
0.0588
AC:
37907
AN:
644996
Hom.:
2886
AF XY:
0.0598
AC XY:
19702
AN XY:
329466
show subpopulations
Gnomad4 AFR exome
AF:
0.0105
Gnomad4 AMR exome
AF:
0.131
Gnomad4 ASJ exome
AF:
0.0429
Gnomad4 EAS exome
AF:
0.368
Gnomad4 SAS exome
AF:
0.0855
Gnomad4 FIN exome
AF:
0.0522
Gnomad4 NFE exome
AF:
0.0347
Gnomad4 OTH exome
AF:
0.0575
GnomAD4 genome
AF:
0.0504
AC:
7665
AN:
152208
Hom.:
535
Cov.:
33
AF XY:
0.0549
AC XY:
4088
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.0110
Gnomad4 AMR
AF:
0.119
Gnomad4 ASJ
AF:
0.0467
Gnomad4 EAS
AF:
0.345
Gnomad4 SAS
AF:
0.0945
Gnomad4 FIN
AF:
0.0518
Gnomad4 NFE
AF:
0.0336
Gnomad4 OTH
AF:
0.0630
Alfa
AF:
0.0399
Hom.:
32
Bravo
AF:
0.0546
Asia WGS
AF:
0.165
AC:
574
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
0.046
DANN
Benign
0.67

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: rs3732443; hg19: chr3-73016584; COSMIC: COSV67474219; API