rs7989336

Variant names:

• chr13-96365294-G-A
• rs7989336
• NM_153456.4:c.707+273725G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-96365294-G-A
• chr13-96365294-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_153456.4(HS6ST3):​c.707+273725G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 152,032 control chromosomes in the GnomAD database, including 21,744 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 0.53 (21744 hom., cov: 32)
• Consequence: HS6ST3 NM_153456.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657
• Publications: 27 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153456.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HS6ST3	NM_153456.4	MANE Select	c.707+273725G>A		intron	N/A	NP_703157.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HS6ST3	ENST00000376705.4	TSL:1 MANE Select	c.707+273725G>A		intron	N/A	ENSP00000365895.2

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80148 AN: 151914 Hom.: 21709 Cov.: 32

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.528 AC: 80229 AN: 152032 Hom.: 21744 Cov.: 32 AF XY: 0.529 AC XY: 39291 AN XY: 74290

African (AFR) AF: 0.630 AC: 26125 AN: 41492

American (AMR) AF: 0.387 AC: 5907 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2130 AN: 3468

East Asian (EAS) AF: 0.493 AC: 2539 AN: 5152

South Asian (SAS) AF: 0.584 AC: 2815 AN: 4822

European-Finnish (FIN) AF: 0.564 AC: 5945 AN: 10542

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32907 AN: 67974

Other (OTH) AF: 0.539 AC: 1137 AN: 2110

Alfa AF: 0.491 Hom.: 26627

Bravo AF: 0.511

Asia WGS AF: 0.576 AC: 2003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.40
PhyloP100		-0.66
Mutation Taster		=100/0	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: rs7989336; hg19: chr13-97017548;