rs13211840

Variant names:

• chr6-148791054-T-C
• rs13211840
• NM_005715.3:c.247+43377T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005715.3(UST):​c.247+43377T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,244 control chromosomes in the GnomAD database, including 1,966 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 0.15 (1966 hom., cov: 32)
• Consequence: UST NM_005715.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651
• Publications: 4 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 -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 = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UST	NM_005715.3	c.247+43377T>C		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+43377T>C		intron_variant	Intron 1 of 7	1	NM_005715.3	ENSP00000356433.4

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22527 AN: 152126 Hom.: 1953 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0781

Gnomad EAS AF: 0.00520

Gnomad SAS AF: 0.0598

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.148 AC: 22578 AN: 152244 Hom.: 1966 Cov.: 32 AF XY: 0.143 AC XY: 10671 AN XY: 74444

African (AFR) AF: 0.228 AC: 9461 AN: 41524

American (AMR) AF: 0.109 AC: 1672 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0781 AC: 271 AN: 3472

East Asian (EAS) AF: 0.00521 AC: 27 AN: 5184

South Asian (SAS) AF: 0.0599 AC: 289 AN: 4828

European-Finnish (FIN) AF: 0.129 AC: 1372 AN: 10606

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9185 AN: 68006

Other (OTH) AF: 0.133 AC: 282 AN: 2116

Alfa AF: 0.136 Hom.: 776

Bravo AF: 0.150

Asia WGS AF: 0.0530 AC: 182 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	1.4
DANN	Benign	0.70
PhyloP100		-0.65
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: rs13211840; hg19: chr6-149112190;