rs6929401

Positions:

• chr6-148795720-C-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+48043C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,030 control chromosomes in the GnomAD database, including 1,406 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 0.13 (1406 hom., cov: 32)
• Consequence: UST NM_005715.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UST	NM_005715.3	c.247+48043C>T		intron_variant		ENST00000367463.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UST	ENST00000367463.5	c.247+48043C>T		intron_variant		1	NM_005715.3	P1

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19194 AN: 151912 Hom.: 1404 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0859

Gnomad ASJ AF: 0.0547

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.0939

Gnomad FIN AF: 0.0529

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.126 AC: 19221 AN: 152030 Hom.: 1406 Cov.: 32 AF XY: 0.124 AC XY: 9225 AN XY: 74320

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.0857

Gnomad4 ASJ AF: 0.0547

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.0938

Gnomad4 FIN AF: 0.0529

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.118

Alfa AF: 0.106 Hom.: 506

Bravo AF: 0.133

Asia WGS AF: 0.0940 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs6929401; hg19: chr6-149116856;