rs2067082

chr3-38396691-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005108.4(XYLB):c.1351-381G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 152,096 control chromosomes in the GnomAD database, including 16,574 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 0.44 (16574 hom., cov: 32)
• Consequence: XYLB NM_005108.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• 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/exons	MANE	UniProt
XYLB	NM_005108.4	c.1351-381G>C		intron_variant		ENST00000207870.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XYLB	ENST00000207870.8	c.1351-381G>C		intron_variant		1	NM_005108.4	P1

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66903 AN: 151978 Hom.: 16575 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.440 AC: 66907 AN: 152096 Hom.: 16574 Cov.: 32 AF XY: 0.438 AC XY: 32527 AN XY: 74330

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.464

Alfa AF: 0.499 Hom.: 2540

Bravo AF: 0.413

Asia WGS AF: 0.395 AC: 1372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.65

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

Other links and lift over

dbSNP: rs2067082; hg19: chr3-38438182;