rs9513122

Variant names:

• chr13-96348280-A-G
• rs9513122
• NM_153456.4:c.707+256711A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_153456.4(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 NM_153456.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.591
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
HS6ST3	NM_153456.4	c.707+256711A>G		intron_variant	Intron 1 of 1	ENST00000376705.4	NP_703157.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HS6ST3	ENST00000376705.4	c.707+256711A>G		intron_variant	Intron 1 of 1	1	NM_153456.4	ENSP00000365895.2

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47936 AN: 152030 Hom.: 8477 Cov.: 32

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

African (AFR) AF: 0.149 AC: 6169 AN: 41534

American (AMR) AF: 0.380 AC: 5818 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 818 AN: 3468

East Asian (EAS) AF: 0.325 AC: 1678 AN: 5162

South Asian (SAS) AF: 0.326 AC: 1572 AN: 4828

European-Finnish (FIN) AF: 0.358 AC: 3792 AN: 10584

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.400 AC: 27217 AN: 67966

Other (OTH) AF: 0.304 AC: 642 AN: 2110

Alfa AF: 0.370 Hom.: 18505

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
PhyloP100		0.59
Mutation Taster		=99/1	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: rs9513122; hg19: chr13-97000534;