rs2070488

Variant summary

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

The NM_005108.4(XYLB):​c.1533+14G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 1,611,952 control chromosomes in the GnomAD database, including 226,652 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 0.43 ( 16049 hom., cov: 32)
Exomes 𝑓: 0.53 ( 210603 hom. )

Consequence

XYLB
NM_005108.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.713
Variant links:
Genes affected
XYLB (HGNC:12839): (xylulokinase) The protein encoded by this gene shares 22% sequence identity with Hemophilus influenzae xylulokinase, and even higher identity to other gene products in C.elegans (45%) and yeast (31-35%), which are thought to belong to a family of enzymes that include fucokinase, gluconokinase, glycerokinase and xylulokinase. These proteins play important roles in energy metabolism. [provided by RefSeq, Aug 2009]

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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
XYLBNM_005108.4 linkuse as main transcriptc.1533+14G>A intron_variant ENST00000207870.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
XYLBENST00000207870.8 linkuse as main transcriptc.1533+14G>A intron_variant 1 NM_005108.4 P1O75191-1

Frequencies

GnomAD3 genomes
AF:
0.431
AC:
65562
AN:
151986
Hom.:
16051
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.210
Gnomad AMI
AF:
0.464
Gnomad AMR
AF:
0.387
Gnomad ASJ
AF:
0.494
Gnomad EAS
AF:
0.270
Gnomad SAS
AF:
0.505
Gnomad FIN
AF:
0.526
Gnomad MID
AF:
0.475
Gnomad NFE
AF:
0.564
Gnomad OTH
AF:
0.451
GnomAD3 exomes
AF:
0.475
AC:
119278
AN:
251274
Hom.:
30325
AF XY:
0.488
AC XY:
66222
AN XY:
135794
show subpopulations
Gnomad AFR exome
AF:
0.208
Gnomad AMR exome
AF:
0.333
Gnomad ASJ exome
AF:
0.501
Gnomad EAS exome
AF:
0.267
Gnomad SAS exome
AF:
0.517
Gnomad FIN exome
AF:
0.529
Gnomad NFE exome
AF:
0.564
Gnomad OTH exome
AF:
0.496
GnomAD4 exome
AF:
0.530
AC:
774181
AN:
1459848
Hom.:
210603
Cov.:
32
AF XY:
0.531
AC XY:
385811
AN XY:
726368
show subpopulations
Gnomad4 AFR exome
AF:
0.197
Gnomad4 AMR exome
AF:
0.339
Gnomad4 ASJ exome
AF:
0.496
Gnomad4 EAS exome
AF:
0.302
Gnomad4 SAS exome
AF:
0.518
Gnomad4 FIN exome
AF:
0.536
Gnomad4 NFE exome
AF:
0.560
Gnomad4 OTH exome
AF:
0.499
GnomAD4 genome
AF:
0.431
AC:
65570
AN:
152104
Hom.:
16049
Cov.:
32
AF XY:
0.428
AC XY:
31847
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.210
Gnomad4 AMR
AF:
0.387
Gnomad4 ASJ
AF:
0.494
Gnomad4 EAS
AF:
0.270
Gnomad4 SAS
AF:
0.506
Gnomad4 FIN
AF:
0.526
Gnomad4 NFE
AF:
0.564
Gnomad4 OTH
AF:
0.450
Alfa
AF:
0.518
Hom.:
27446
Bravo
AF:
0.406
Asia WGS
AF:
0.399
AC:
1386
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.51
DANN
Benign
0.47
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs2070488; hg19: chr3-38442490; API