rs952481
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152531.5(XXYLT1):c.786-31258A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,248 control chromosomes in the GnomAD database, including 4,240 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 0.23 ( 4240 hom., cov: 32)
Consequence
XXYLT1
NM_152531.5 intron
NM_152531.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.12
Publications
5 publications found
Genes affected
XXYLT1 (HGNC:26639): (xyloside xylosyltransferase 1) Enables magnesium ion binding activity; manganese ion binding activity; and xylosyl alpha-1,3-xylosyltransferase activity. Involved in O-glycan processing. Is integral component of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.231 AC: 35088AN: 152130Hom.: 4240 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
35088
AN:
152130
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.231 AC: 35113AN: 152248Hom.: 4240 Cov.: 32 AF XY: 0.231 AC XY: 17212AN XY: 74428 show subpopulations
GnomAD4 genome
AF:
AC:
35113
AN:
152248
Hom.:
Cov.:
32
AF XY:
AC XY:
17212
AN XY:
74428
show subpopulations
African (AFR)
AF:
AC:
10830
AN:
41552
American (AMR)
AF:
AC:
2805
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
AC:
442
AN:
3472
East Asian (EAS)
AF:
AC:
2200
AN:
5172
South Asian (SAS)
AF:
AC:
1820
AN:
4832
European-Finnish (FIN)
AF:
AC:
2007
AN:
10594
Middle Eastern (MID)
AF:
AC:
61
AN:
294
European-Non Finnish (NFE)
AF:
AC:
14288
AN:
68012
Other (OTH)
AF:
AC:
495
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1448
2896
4344
5792
7240
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
386
772
1158
1544
1930
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1307
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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