chr3-38396691-G-C

Variant names:

• chr3-38396691-G-C
• rs2067082
• NM_005108.4:c.1351-381G>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.1351-381G>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
• Publications: 6 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005108.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XYLB	NM_005108.4	MANE Select	c.1351-381G>C		intron	N/A	NP_005099.2
	XYLB	NM_001349178.2		c.1351-381G>C		intron	N/A	NP_001336107.1
	XYLB	NM_001349179.2		c.940-381G>C		intron	N/A	NP_001336108.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XYLB	ENST00000207870.8	TSL:1 MANE Select	c.1351-381G>C		intron	N/A	ENSP00000207870.3
	XYLB	ENST00000650590.1		c.1270-381G>C		intron	N/A	ENSP00000496840.1
	XYLB	ENST00000424034.5	TSL:2	n.*1014-381G>C		intron	N/A	ENSP00000398845.1

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

African (AFR) AF: 0.222 AC: 9210 AN: 41472

American (AMR) AF: 0.395 AC: 6029 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1838 AN: 3470

East Asian (EAS) AF: 0.260 AC: 1345 AN: 5180

South Asian (SAS) AF: 0.510 AC: 2459 AN: 4826

European-Finnish (FIN) AF: 0.550 AC: 5816 AN: 10572

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38658 AN: 67978

Other (OTH) AF: 0.464 AC: 982 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.65
PhyloP100		-0.51
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: rs2067082; hg19: chr3-38438182;