rs1594160

chr2-31356103-A-Cchr2-31356103-A-Gchr2-31356103-A-T

Variant summary

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

The NM_000379.4(XDH):c.2632-5880T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.743 in 152,012 control chromosomes in the GnomAD database, including 42,012 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 0.74 (42012 hom., cov: 31)
• Consequence: XDH NM_000379.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XDH	NM_000379.4	c.2632-5880T>G		intron_variant		ENST00000379416.4
XDH	XM_011533095.3	c.2629-5880T>G		intron_variant
XDH	XM_011533096.3	c.2632-5880T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XDH	ENST00000379416.4	c.2632-5880T>G		intron_variant		1	NM_000379.4	P1

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112824 AN: 151896 Hom.: 41988 Cov.: 31

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.743 AC: 112896 AN: 152012 Hom.: 42012 Cov.: 31 AF XY: 0.742 AC XY: 55135 AN XY: 74310

Gnomad4 AFR AF: 0.791

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.849

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.723

Alfa AF: 0.733 Hom.: 7098

Bravo AF: 0.749

Asia WGS AF: 0.735 AC: 2555 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.3
Dann	Benign	0.55

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: rs1594160; hg19: chr2-31578969;