Variant 2-31365571-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000379.4(XDH):c.2457-27G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0288 in 1,613,606 control chromosomes in the GnomAD database, including 1,007 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.024 ( 83 hom., cov: 32)

Exomes 𝑓: 0.029 ( 924 hom. )

Consequence

XDH
NM_000379.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.400

Variant links:

Genes affected

XDH (HGNC:12805): (xanthine dehydrogenase) Xanthine dehydrogenase belongs to the group of molybdenum-containing hydroxylases involved in the oxidative metabolism of purines. The encoded protein has been identified as a moonlighting protein based on its ability to perform mechanistically distinct functions. Xanthine dehydrogenase can be converted to xanthine oxidase by reversible sulfhydryl oxidation or by irreversible proteolytic modification. Defects in xanthine dehydrogenase cause xanthinuria, may contribute to adult respiratory stress syndrome, and may potentiate influenza infection through an oxygen metabolite-dependent mechanism. [provided by RefSeq, Jan 2014]

XDH links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 2-31365571-C-T is Benign according to our data. Variant chr2-31365571-C-T is described in ClinVar as [Benign]. Clinvar id is 1283317.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
XDH	NM_000379.4 linkuse as main transcript	c.2457-27G>A	intron_variant	ENST00000379416.4
XDH	XM_011533095.3 linkuse as main transcript	c.2454-27G>A	intron_variant
XDH	XM_011533096.3 linkuse as main transcript	c.2457-27G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XDH	ENST00000379416.4 linkuse as main transcript	c.2457-27G>A		intron_variant		1	NM_000379.4	P1

Frequencies

GnomAD3 genomes

AF:

0.0243

AC:

3694

AN:

152166

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00741

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0200

Gnomad ASJ

AF:

0.0239

Gnomad EAS

AF:

0.117

Gnomad SAS

AF:

0.0601

Gnomad FIN

AF:

0.0123

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0277

Gnomad OTH

AF:

0.0301

GnomAD3 exomes

AF:

0.0334

AC:

8374

AN:

250772

Hom.:

261

AF XY:

0.0357

AC XY:

4833

AN XY:

135512

show subpopulations

Gnomad AFR exome

AF:

0.00622

Gnomad AMR exome

AF:

0.0137

Gnomad ASJ exome

AF:

0.0207

Gnomad EAS exome

AF:

0.130

Gnomad SAS exome

AF:

0.0571

Gnomad FIN exome

AF:

0.0106

Gnomad NFE exome

AF:

0.0266

Gnomad OTH exome

AF:

0.0343

GnomAD4 exome

AF:

0.0293

AC:

42787

AN:

1461322

Hom.:

924

Cov.:

AF XY:

0.0300

AC XY:

21833

AN XY:

727038

show subpopulations

Gnomad4 AFR exome

AF:

0.00574

Gnomad4 AMR exome

AF:

0.0146

Gnomad4 ASJ exome

AF:

0.0184

Gnomad4 EAS exome

AF:

0.117

Gnomad4 SAS exome

AF:

0.0557

Gnomad4 FIN exome

AF:

0.0125

Gnomad4 NFE exome

AF:

0.0261

Gnomad4 OTH exome

AF:

0.0348

GnomAD4 genome

AF:

0.0242

AC:

3692

AN:

152284

Hom.:

Cov.:

AF XY:

0.0248

AC XY:

1844

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.00741

Gnomad4 AMR

AF:

0.0200

Gnomad4 ASJ

AF:

0.0239

Gnomad4 EAS

AF:

0.117

Gnomad4 SAS

AF:

0.0605

Gnomad4 FIN

AF:

0.0123

Gnomad4 NFE

AF:

0.0277

Gnomad4 OTH

AF:

0.0298

Alfa

AF:

0.0154

Hom.:

Bravo

AF:

0.0227

Asia WGS

AF:

0.0700

AC:

244

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 07, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.4

DANN

Benign

0.72

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over