13-96579016-A-G

Position:

• chr13-96579016-A-G

Variant summary

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

The NM_153456.4(HS6ST3):​c.708-253474A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 152,086 control chromosomes in the GnomAD database, including 53,509 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 0.83 (53509 hom., cov: 31)
• Consequence: HS6ST3 NM_153456.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.311

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HS6ST3	NM_153456.4	c.708-253474A>G		intron_variant		ENST00000376705.4	NP_703157.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HS6ST3	ENST00000376705.4	c.708-253474A>G		intron_variant		1	NM_153456.4	ENSP00000365895.2

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126674 AN: 151968 Hom.: 53482 Cov.: 31

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.833 AC: 126750 AN: 152086 Hom.: 53509 Cov.: 31 AF XY: 0.835 AC XY: 62087 AN XY: 74334

Gnomad4 AFR AF: 0.689

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 0.913

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.881

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.897

Gnomad4 OTH AF: 0.842

Alfa AF: 0.886 Hom.: 114356

Bravo AF: 0.825

Asia WGS AF: 0.803 AC: 2790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	7.4
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: rs547571; hg19: chr13-97231270;