rs1858740

Variant names:

• chr3-38396881-T-C
• rs1858740
• NM_005108.4:c.1351-191T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005108.4(XYLB):​c.1351-191T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 152,024 control chromosomes in the GnomAD database, including 16,278 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 (16278 hom., cov: 31)
• Consequence: XYLB NM_005108.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.718
• Publications: 11 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
XYLB	NM_005108.4	c.1351-191T>C		intron_variant	Intron 16 of 18	ENST00000207870.8	NP_005099.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XYLB	ENST00000207870.8	c.1351-191T>C		intron_variant	Intron 16 of 18	1	NM_005108.4	ENSP00000207870.3

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65399 AN: 151906 Hom.: 16279 Cov.: 31

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.462

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.430 AC: 65399 AN: 152024 Hom.: 16278 Cov.: 31 AF XY: 0.428 AC XY: 31808 AN XY: 74292

African (AFR) AF: 0.187 AC: 7741 AN: 41476

American (AMR) AF: 0.393 AC: 6005 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1840 AN: 3472

East Asian (EAS) AF: 0.259 AC: 1338 AN: 5162

South Asian (SAS) AF: 0.511 AC: 2462 AN: 4818

European-Finnish (FIN) AF: 0.550 AC: 5802 AN: 10556

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.569 AC: 38664 AN: 67960

Other (OTH) AF: 0.462 AC: 975 AN: 2112

Alfa AF: 0.526 Hom.: 11223

Bravo AF: 0.401

Asia WGS AF: 0.395 AC: 1373 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	0.98
DANN	Benign	0.38
PhyloP100		-0.72
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1858740; hg19: chr3-38438372;