NM_153456.4:c.707+366359G>A

Variant names:

• chr13-96457928-G-A
• rs8002510
• NM_153456.4:c.707+366359G>A

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+366359G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0607 in 151,646 control chromosomes in the GnomAD database, including 368 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 0.061 (368 hom., cov: 32)
• Consequence: HS6ST3 NM_153456.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0989 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HS6ST3	NM_153456.4	c.707+366359G>A		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+366359G>A		intron_variant	Intron 1 of 1	1	NM_153456.4	ENSP00000365895.2

Frequencies

GnomAD3 genomes AF: 0.0606 AC: 9183 AN: 151528 Hom.: 361 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0369

Gnomad ASJ AF: 0.0666

Gnomad EAS AF: 0.0979

Gnomad SAS AF: 0.0689

Gnomad FIN AF: 0.0706

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0370

Gnomad OTH AF: 0.0469

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

GnomAD4 genome AF: 0.0607 AC: 9210 AN: 151646 Hom.: 368 Cov.: 32 AF XY: 0.0614 AC XY: 4551 AN XY: 74064

African (AFR) AF: 0.101 AC: 4189 AN: 41276

American (AMR) AF: 0.0368 AC: 562 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0666 AC: 231 AN: 3470

East Asian (EAS) AF: 0.0988 AC: 508 AN: 5144

South Asian (SAS) AF: 0.0706 AC: 339 AN: 4802

European-Finnish (FIN) AF: 0.0706 AC: 738 AN: 10458

Middle Eastern (MID) AF: 0.0377 AC: 11 AN: 292

European-Non Finnish (NFE) AF: 0.0370 AC: 2514 AN: 67928

Other (OTH) AF: 0.0535 AC: 113 AN: 2112

Alfa AF: 0.0457 Hom.: 77

Bravo AF: 0.0602

Asia WGS AF: 0.105 AC: 362 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.52
DANN	Benign	0.62
PhyloP100		-0.61
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: rs8002510; hg19: chr13-97110182;