6-149008131-A-G

Position:

• chr6-149008131-A-G

Variant summary

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

The NM_005715.3(UST):​c.682-11008A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 152,272 control chromosomes in the GnomAD database, including 64,917 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 0.92 (64917 hom., cov: 31)
• Consequence: UST NM_005715.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.295

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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UST	NM_005715.3	c.682-11008A>G		intron_variant		ENST00000367463.5
UST	XM_047418047.1	c.*5-11008A>G		intron_variant
UST	XR_001743088.3	n.1221-3826A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UST	ENST00000367463.5	c.682-11008A>G		intron_variant		1	NM_005715.3	P1

Frequencies

GnomAD3 genomes AF: 0.921 AC: 140073 AN: 152154 Hom.: 64863 Cov.: 31

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.925

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.950

Gnomad OTH AF: 0.913

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

GnomAD4 genome AF: 0.921 AC: 140186 AN: 152272 Hom.: 64917 Cov.: 31 AF XY: 0.917 AC XY: 68306 AN XY: 74456

Gnomad4 AFR AF: 0.936

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.925

Gnomad4 FIN AF: 0.968

Gnomad4 NFE AF: 0.950

Gnomad4 OTH AF: 0.912

Alfa AF: 0.938 Hom.: 104191

Bravo AF: 0.904

Asia WGS AF: 0.869 AC: 3020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.3
DANN	Benign	0.70

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: rs2500535; hg19: chr6-149329267; COSMIC: COSV66546525; COSMIC: COSV66546525;