dbSNP rs17279736: UXS1:c.472+4281C>G (chr2-106140909-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001253875.2(UXS1):c.472+4281C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,074 control chromosomes in the GnomAD database, including 5,084 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 0.25 ( 5084 hom., cov: 32)

Consequence

UXS1
NM_001253875.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.692

Variant links:

Genes affected

UXS1 (HGNC:17729): (UDP-glucuronate decarboxylase 1) This gene encodes an enzyme found in the perinuclear Golgi which catalyzes the synthesis of UDP-xylose used in glycosaminoglycan (GAG) synthesis on proteoglycans. The GAG chains are covalently attached to proteoglycans which participate in signaling pathways during development. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2014]

UXS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UXS1	NM_001253875.2 link	c.472+4281C>G		intron_variant	Intron 6 of 14	ENST00000283148.12	NP_001240804.1	Q8NBZ7-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UXS1	ENST00000283148.12 link	c.472+4281C>G		intron_variant	Intron 6 of 14	2	NM_001253875.2	ENSP00000283148.7		Q8NBZ7-2

Frequencies

GnomAD3 genomes

AF:

0.248

AC:

37671

AN:

151954

Hom.:

5081

Cov.:

show subpopulations

Gnomad AFR

AF:

0.192

Gnomad AMI

AF:

0.146

Gnomad AMR

AF:

0.204

Gnomad ASJ

AF:

0.388

Gnomad EAS

AF:

0.0674

Gnomad SAS

AF:

0.206

Gnomad FIN

AF:

0.224

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.307

Gnomad OTH

AF:

0.245

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

GnomAD4 genome

AF:

0.248

AC:

37703

AN:

152074

Hom.:

5084

Cov.:

AF XY:

0.242

AC XY:

17957

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.192

Gnomad4 AMR

AF:

0.203

Gnomad4 ASJ

AF:

0.388

Gnomad4 EAS

AF:

0.0675

Gnomad4 SAS

AF:

0.206

Gnomad4 FIN

AF:

0.224

Gnomad4 NFE

AF:

0.307

Gnomad4 OTH

AF:

0.241

Alfa

AF:

0.272

Hom.:

706

Bravo

AF:

0.243

Asia WGS

AF:

0.131

AC:

458

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.2

DANN

Benign

0.43

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over