rs13211840

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.651
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
USTNM_005715.3 linkuse as main transcriptc.247+43377T>C intron_variant ENST00000367463.5 NP_005706.1 Q9Y2C2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
USTENST00000367463.5 linkuse as main transcriptc.247+43377T>C intron_variant 1 NM_005715.3 ENSP00000356433.4 Q9Y2C2

Frequencies

GnomAD3 genomes
AF:
0.148
AC:
22527
AN:
152126
Hom.:
1953
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.228
Gnomad4 AMR
AF:
0.109
Gnomad4 ASJ
AF:
0.0781
Gnomad4 EAS
AF:
0.00521
Gnomad4 SAS
AF:
0.0599
Gnomad4 FIN
AF:
0.129
Gnomad4 NFE
AF:
0.135
Gnomad4 OTH
AF:
0.133
Alfa
AF:
0.137
Hom.:
489
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

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs13211840; hg19: chr6-149112190; API