chr6-148935303-A-G

Variant names:

• chr6-148935303-A-G
• rs17666460
• NM_005715.3:c.292-5976A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
UST	NM_005715.3	c.292-5976A>G		intron_variant	Intron 2 of 7	ENST00000367463.5	NP_005706.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UST	ENST00000367463.5	c.292-5976A>G		intron_variant	Intron 2 of 7	1	NM_005715.3	ENSP00000356433.4

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

African (AFR) AF: 0.0188 AC: 780 AN: 41596

American (AMR) AF: 0.0718 AC: 1099 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 495 AN: 3470

East Asian (EAS) AF: 0.000770 AC: 4 AN: 5194

South Asian (SAS) AF: 0.0224 AC: 108 AN: 4826

European-Finnish (FIN) AF: 0.0481 AC: 511 AN: 10624

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6858 AN: 68022

Other (OTH) AF: 0.0803 AC: 170 AN: 2116

Alfa AF: 0.0619 Hom.: 169

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
PhyloP100		0.66
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17666460; hg19: chr6-149256439;