rs13219957

chr6-148949693-G-A

Variant summary

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

The NM_005715.3(UST):c.448-4179G>A 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 152,130 control chromosomes in the GnomAD database, including 1,415 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 (1415 hom., cov: 31)
• Consequence: UST NM_005715.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591

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 (AMR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UST	NM_005715.3	c.448-4179G>A		intron_variant		ENST00000367463.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UST	ENST00000367463.5	c.448-4179G>A		intron_variant		1	NM_005715.3	P1

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19181 AN: 152012 Hom.: 1417 Cov.: 31

Gnomad AFR AF: 0.0515

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.126 AC: 19191 AN: 152130 Hom.: 1415 Cov.: 31 AF XY: 0.125 AC XY: 9295 AN XY: 74364

Gnomad4 AFR AF: 0.0514

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.130

Alfa AF: 0.150 Hom.: 2484

Bravo AF: 0.128

Asia WGS AF: 0.118 AC: 413 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	5.0
Dann	Benign	0.58

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: rs13219957; hg19: chr6-149270829;