Variant 18-36187786-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_017947.4(MOCOS):c.142+105G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 1,197,382 control chromosomes in the GnomAD database, including 62,985 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.29 ( 6695 hom., cov: 33)

Exomes 𝑓: 0.33 ( 56290 hom. )

Consequence

MOCOS
NM_017947.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.68

Variant links:

Genes affected

MOCOS (HGNC:18234): (molybdenum cofactor sulfurase) This gene encodes an enzyme that sulfurates the molybdenum cofactor which is required for activation of the xanthine dehydrogenase (XDH) and aldehyde oxidase (AO) enzymes. XDH catalyzes the conversion of hypoxanthine to uric acid via xanthine, as well as the conversion of allopurinol to oxypurinol, and pyrazinamide to 5-hydroxy pyrazinamide. Mutations in this gene cause the metabolic disorder classical xanthinuria type II which is characterized by the loss of XDH/XO and AO enzyme activity, decreased levels of uric acid in the urine, increased levels of xanthine and hypoxanthine in the serum and urine, formation of xanthine stones in the urinary tract, and myositis due to tissue deposition of xanthine. [provided by RefSeq, Apr 2017]

MOCOS links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 18-36187786-G-A is Benign according to our data. Variant chr18-36187786-G-A is described in ClinVar as [Benign]. Clinvar id is 1289610.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOCOS	NM_017947.4 linkuse as main transcript	c.142+105G>A		intron_variant		ENST00000261326.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOCOS	ENST00000261326.6 linkuse as main transcript	c.142+105G>A		intron_variant		1	NM_017947.4	P1

Frequencies

GnomAD3 genomes

AF:

0.288

AC:

43833

AN:

151968

Hom.:

6702

Cov.:

show subpopulations

Gnomad AFR

AF:

0.192

Gnomad AMI

AF:

0.291

Gnomad AMR

AF:

0.330

Gnomad ASJ

AF:

0.318

Gnomad EAS

AF:

0.169

Gnomad SAS

AF:

0.166

Gnomad FIN

AF:

0.354

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.343

Gnomad OTH

AF:

0.296

GnomAD4 exome

AF:

0.326

AC:

340596

AN:

1045294

Hom.:

56290

AF XY:

0.325

AC XY:

161042

AN XY:

495022

show subpopulations

Gnomad4 AFR exome

AF:

0.189

Gnomad4 AMR exome

AF:

0.345

Gnomad4 ASJ exome

AF:

0.327

Gnomad4 EAS exome

AF:

0.195

Gnomad4 SAS exome

AF:

0.169

Gnomad4 FIN exome

AF:

0.348

Gnomad4 NFE exome

AF:

0.337

Gnomad4 OTH exome

AF:

0.299

GnomAD4 genome

AF:

0.288

AC:

43839

AN:

152088

Hom.:

6695

Cov.:

AF XY:

0.287

AC XY:

21376

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.192

Gnomad4 AMR

AF:

0.330

Gnomad4 ASJ

AF:

0.318

Gnomad4 EAS

AF:

0.168

Gnomad4 SAS

AF:

0.167

Gnomad4 FIN

AF:

0.354

Gnomad4 NFE

AF:

0.343

Gnomad4 OTH

AF:

0.294

Alfa

AF:

0.323

Hom.:

11070

Bravo

AF:

0.285

Asia WGS

AF:

0.194

AC:

677

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

Jan 23, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

DANN

Benign

0.92

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