rs8002510

chr13-96457928-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+366359G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0607 in 151,646 control chromosomes in the GnomAD database, including 368 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 0.061 (368 hom., cov: 32)
• Consequence: HS6ST3 NM_153456.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0989 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HS6ST3	NM_153456.4	c.707+366359G>A		intron_variant		ENST00000376705.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HS6ST3	ENST00000376705.4	c.707+366359G>A		intron_variant		1	NM_153456.4	P1

Frequencies

GnomAD3 genomes AF: 0.0606 AC: 9183 AN: 151528 Hom.: 361 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0369

Gnomad ASJ AF: 0.0666

Gnomad EAS AF: 0.0979

Gnomad SAS AF: 0.0689

Gnomad FIN AF: 0.0706

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0370

Gnomad OTH AF: 0.0469

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

GnomAD4 genome AF: 0.0607 AC: 9210 AN: 151646 Hom.: 368 Cov.: 32 AF XY: 0.0614 AC XY: 4551 AN XY: 74064

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.0368

Gnomad4 ASJ AF: 0.0666

Gnomad4 EAS AF: 0.0988

Gnomad4 SAS AF: 0.0706

Gnomad4 FIN AF: 0.0706

Gnomad4 NFE AF: 0.0370

Gnomad4 OTH AF: 0.0535

Alfa AF: 0.0466 Hom.: 47

Bravo AF: 0.0602

Asia WGS AF: 0.105 AC: 362 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.52
Dann	Benign	0.62

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: rs8002510; hg19: chr13-97110182;