rs17666460

chr6-148935303-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_005715.3(UST):c.292-5976A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0666 in 152,356 control chromosomes in the GnomAD database, including 489 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 0.067 (489 hom., cov: 32)
• Consequence: UST NM_005715.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.662

Genes affected

UST (HGNC:17223): (uronyl 2-sulfotransferase) Uronyl 2-sulfotransferase transfers sulfate to the 2-position of uronyl residues, such as iduronyl residues in dermatan sulfate and glucuronyl residues in chondroitin sulfate (Kobayashi et al., 1999 [PubMed 10187838]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0988 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UST	NM_005715.3	c.292-5976A>G		intron_variant		ENST00000367463.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UST	ENST00000367463.5	c.292-5976A>G		intron_variant		1	NM_005715.3	P1

Frequencies

GnomAD3 genomes AF: 0.0667 AC: 10155 AN: 152238 Hom.: 489 Cov.: 32

Gnomad AFR AF: 0.0188

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0720

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.000768

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0481

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0812

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

GnomAD4 genome AF: 0.0666 AC: 10149 AN: 152356 Hom.: 489 Cov.: 32 AF XY: 0.0629 AC XY: 4683 AN XY: 74498

Gnomad4 AFR AF: 0.0188

Gnomad4 AMR AF: 0.0718

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.000770

Gnomad4 SAS AF: 0.0224

Gnomad4 FIN AF: 0.0481

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0803

Alfa AF: 0.0794 Hom.: 80

Bravo AF: 0.0656

Asia WGS AF: 0.00924 AC: 32 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
Cadd	Benign	14
Dann	Benign	0.61

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: rs17666460; hg19: chr6-149256439;