6-148792921-G-T

Variant names:

• chr6-148792921-G-T
• rs922898
• NM_005715.3:c.247+45244G>T

Variant summary

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

The NM_005715.3(UST):​c.247+45244G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0921 in 152,132 control chromosomes in the GnomAD database, including 714 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 0.092 (714 hom., cov: 32)
• Consequence: UST NM_005715.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UST	NM_005715.3	c.247+45244G>T		intron_variant	Intron 1 of 7	ENST00000367463.5	NP_005706.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UST	ENST00000367463.5	c.247+45244G>T		intron_variant	Intron 1 of 7	1	NM_005715.3	ENSP00000356433.4

Frequencies

GnomAD3 genomes AF: 0.0922 AC: 14021 AN: 152014 Hom.: 716 Cov.: 32

Gnomad AFR AF: 0.0644

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0829

Gnomad ASJ AF: 0.0557

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0720

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0930

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

GnomAD4 genome AF: 0.0921 AC: 14015 AN: 152132 Hom.: 714 Cov.: 32 AF XY: 0.0934 AC XY: 6949 AN XY: 74370

Gnomad4 AFR AF: 0.0644

Gnomad4 AMR AF: 0.0828

Gnomad4 ASJ AF: 0.0557

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0720

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0920

Alfa AF: 0.0857 Hom.: 359

Bravo AF: 0.0937

Asia WGS AF: 0.137 AC: 475 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.4
DANN	Benign	0.57

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: rs922898; hg19: chr6-149114057;