chr13-96579016-A-G

Variant names:

• chr13-96579016-A-G
• rs547571
• NM_153456.4:c.708-253474A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153456.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HS6ST3	NM_153456.4	MANE Select	c.708-253474A>G		intron	N/A	NP_703157.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HS6ST3	ENST00000376705.4	TSL:1 MANE Select	c.708-253474A>G		intron	N/A	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

African (AFR) AF: 0.689 AC: 28522 AN: 41424

American (AMR) AF: 0.889 AC: 13581 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.913 AC: 3166 AN: 3468

East Asian (EAS) AF: 0.727 AC: 3757 AN: 5166

South Asian (SAS) AF: 0.881 AC: 4254 AN: 4826

European-Finnish (FIN) AF: 0.910 AC: 9630 AN: 10586

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.897 AC: 60991 AN: 68014

Other (OTH) AF: 0.842 AC: 1781 AN: 2114

Alfa AF: 0.877 Hom.: 232699

Bravo AF: 0.825

Asia WGS AF: 0.803 AC: 2790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	7.4
DANN	Benign	0.80
PhyloP100		-0.31
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs547571; hg19: chr13-97231270;