dbSNP rs2070488: XYLB:c.1533+14G>A (chr3-38400999-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.713

Publications

26 publications found

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]

XYLB links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_005108.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.559 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
XYLB	NM_005108.4	MANE Select	c.1533+14G>A	intron	N/A	NP_005099.2
XYLB	NM_001349178.2		c.1533+14G>A	intron	N/A	NP_001336107.1
XYLB	NM_001349179.2		c.1122+14G>A	intron	N/A	NP_001336108.1	O75191-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
XYLB	ENST00000207870.8	TSL:1 MANE Select	c.1533+14G>A	intron	N/A	ENSP00000207870.3	O75191-1
XYLB	ENST00000854437.1		c.1638+14G>A	intron	N/A	ENSP00000524496.1
XYLB	ENST00000650590.1		c.1452+14G>A	intron	N/A	ENSP00000496840.1	A0A3B3IRM4

Frequencies

GnomAD3 genomes

AF:

0.431

AC:

65562

AN:

151986

Hom.:

16051

Cov.:

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

GnomAD2 exomes

AF:

0.475

AC:

119278

AN:

251274

AF XY:

0.488

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 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.:

AF XY:

0.531

AC XY:

385811

AN XY:

726368

show subpopulations

African (AFR)

AF:

0.197

AC:

6598

AN:

33434

American (AMR)

AF:

0.339

AC:

15147

AN:

44706

Ashkenazi Jewish (ASJ)

AF:

0.496

AC:

12950

AN:

26118

East Asian (EAS)

AF:

0.302

AC:

12000

AN:

39684

South Asian (SAS)

AF:

0.518

AC:

44625

AN:

86198

European-Finnish (FIN)

AF:

0.536

AC:

28594

AN:

53396

Middle Eastern (MID)

AF:

0.479

AC:

2757

AN:

5760

European-Non Finnish (NFE)

AF:

0.560

AC:

621415

AN:

1110230

Other (OTH)

AF:

0.499

AC:

30095

AN:

60322

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

18360

36720

55079

73439

91799

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17058

34116

51174

68232

85290

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.431

AC:

65570

AN:

152104

Hom.:

16049

Cov.:

AF XY:

0.428

AC XY:

31847

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.210

AC:

8719

AN:

41478

American (AMR)

AF:

0.387

AC:

5919

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.494

AC:

1714

AN:

3472

East Asian (EAS)

AF:

0.270

AC:

1395

AN:

5168

South Asian (SAS)

AF:

0.506

AC:

2437

AN:

4820

European-Finnish (FIN)

AF:

0.526

AC:

5559

AN:

10572

Middle Eastern (MID)

AF:

0.479

AC:

140

AN:

292

European-Non Finnish (NFE)

AF:

0.564

AC:

38314

AN:

67988

Other (OTH)

AF:

0.450

AC:

951

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1769

3538

5308

7077

8846

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

608

1216

1824

2432

3040

<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:

0.507

Hom.:

65974

Bravo

AF:

0.406

Asia WGS

AF:

0.399

AC:

1386

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.51

(source)

DANN

Benign

0.47

PhyloP100

-0.71

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over