rs1924587

Positions:

• chr13-96745125-G-C
• chr13-96745125-G-T

Variant summary

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

The NM_153456.4(HS6ST3):​c.708-87365G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,850 control chromosomes in the GnomAD database, including 17,728 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 (17728 hom., cov: 32)
• Consequence: HS6ST3 NM_153456.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HS6ST3	NM_153456.4	c.708-87365G>C		intron_variant		ENST00000376705.4	NP_703157.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HS6ST3	ENST00000376705.4	c.708-87365G>C		intron_variant		1	NM_153456.4	ENSP00000365895.2

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72206 AN: 151732 Hom.: 17695 Cov.: 32

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.476 AC: 72285 AN: 151850 Hom.: 17728 Cov.: 32 AF XY: 0.475 AC XY: 35285 AN XY: 74242

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.424

Alfa AF: 0.300 Hom.: 684

Bravo AF: 0.484

Asia WGS AF: 0.355 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.63

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: rs1924587; hg19: chr13-97397379;