13-96365294-G-A

Position:

• chr13-96365294-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HS6ST3	NM_153456.4	c.707+273725G>A		intron_variant		ENST00000376705.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HS6ST3	ENST00000376705.4	c.707+273725G>A		intron_variant		1	NM_153456.4	P1

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

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.539

Alfa AF: 0.391 Hom.: 1168

Bravo AF: 0.511

Asia WGS AF: 0.576 AC: 2003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.40

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: rs7989336; hg19: chr13-97017548;