rs9300341

Positions:

• chr13-96274610-T-A
• chr13-96274610-T-C
• chr13-96274610-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000376705.4(HS6ST3):​c.707+183041T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,724 control chromosomes in the GnomAD database, including 17,788 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 0.48 (17788 hom., cov: 29)
• Consequence: HS6ST3 ENST00000376705.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.876

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=-0.6).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HS6ST3	NM_153456.4	c.707+183041T>A		intron_variant		ENST00000376705.4	NP_703157.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HS6ST3	ENST00000376705.4	c.707+183041T>A		intron_variant		1	NM_153456.4	ENSP00000365895	P1

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73172 AN: 151606 Hom.: 17777 Cov.: 29

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.483 AC: 73209 AN: 151724 Hom.: 17788 Cov.: 29 AF XY: 0.487 AC XY: 36114 AN XY: 74108

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.502

Alfa AF: 0.471 Hom.: 2054

Bravo AF: 0.464

Asia WGS AF: 0.566 AC: 1968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	12
DANN	Benign	0.80

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: rs9300341; hg19: chr13-96926864;