rs9513122

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000376705.4(HS6ST3):​c.707+256711A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,148 control chromosomes in the GnomAD database, including 8,481 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 0.32 ( 8481 hom., cov: 32)

Consequence

HS6ST3
ENST00000376705.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.591
Variant links:
Genes affected
HS6ST3 (HGNC:19134): (heparan sulfate 6-O-sulfotransferase 3) Heparan sulfate (HS) sulfotransferases, such as HS6ST3, modify HS to generate structures required for interactions between HS and a variety of proteins. These interactions are implicated in proliferation and differentiation, adhesion, migration, inflammation, blood coagulation, and other diverse processes (Habuchi et al., 2000 [PubMed 10644753]).[supplied by OMIM, Mar 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.31).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HS6ST3NM_153456.4 linkuse as main transcriptc.707+256711A>G intron_variant ENST00000376705.4 NP_703157.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HS6ST3ENST00000376705.4 linkuse as main transcriptc.707+256711A>G intron_variant 1 NM_153456.4 ENSP00000365895 P1

Frequencies

GnomAD3 genomes
AF:
0.315
AC:
47936
AN:
152030
Hom.:
8477
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.149
Gnomad AMI
AF:
0.189
Gnomad AMR
AF:
0.380
Gnomad ASJ
AF:
0.236
Gnomad EAS
AF:
0.325
Gnomad SAS
AF:
0.327
Gnomad FIN
AF:
0.358
Gnomad MID
AF:
0.191
Gnomad NFE
AF:
0.401
Gnomad OTH
AF:
0.307
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.315
AC:
47935
AN:
152148
Hom.:
8481
Cov.:
32
AF XY:
0.315
AC XY:
23396
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.149
Gnomad4 AMR
AF:
0.380
Gnomad4 ASJ
AF:
0.236
Gnomad4 EAS
AF:
0.325
Gnomad4 SAS
AF:
0.326
Gnomad4 FIN
AF:
0.358
Gnomad4 NFE
AF:
0.400
Gnomad4 OTH
AF:
0.304
Alfa
AF:
0.377
Hom.:
15030
Bravo
AF:
0.313
Asia WGS
AF:
0.282
AC:
978
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.31
CADD
Benign
11
DANN
Benign
0.79

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: rs9513122; hg19: chr13-97000534; API