13-96441315-T-C

Variant names:

• chr13-96441315-T-C
• rs1327914
• NM_153456.4:c.707+349746T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_153456.4(HS6ST3):​c.707+349746T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 151,586 control chromosomes in the GnomAD database, including 3,520 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 0.21 (3520 hom., cov: 30)
• Consequence: HS6ST3 NM_153456.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 3 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=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HS6ST3	NM_153456.4	c.707+349746T>C		intron_variant	Intron 1 of 1	ENST00000376705.4	NP_703157.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HS6ST3	ENST00000376705.4	c.707+349746T>C		intron_variant	Intron 1 of 1	1	NM_153456.4	ENSP00000365895.2

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31361 AN: 151472 Hom.: 3504 Cov.: 30

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.207 AC: 31410 AN: 151586 Hom.: 3520 Cov.: 30 AF XY: 0.204 AC XY: 15104 AN XY: 74046

African (AFR) AF: 0.290 AC: 11974 AN: 41290

American (AMR) AF: 0.154 AC: 2346 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 666 AN: 3464

East Asian (EAS) AF: 0.239 AC: 1232 AN: 5152

South Asian (SAS) AF: 0.169 AC: 806 AN: 4778

European-Finnish (FIN) AF: 0.131 AC: 1381 AN: 10508

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12262 AN: 67892

Other (OTH) AF: 0.222 AC: 465 AN: 2098

Alfa AF: 0.182 Hom.: 2168

Bravo AF: 0.212

Asia WGS AF: 0.205 AC: 716 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.38
DANN	Benign	0.34
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs1327914; hg19: chr13-97093569;