rs9488343

Variant names:

• chr6-114226817-G-A
• rs9488343
• NM_153612.4:c.-145+1768C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-114226817-G-A
• chr6-114226817-G-T

Variant summary

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

The NM_153612.4(HS3ST5):​c.-145+1768C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 151,664 control chromosomes in the GnomAD database, including 14,789 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 0.44 (14789 hom., cov: 32)
• Consequence: HS3ST5 NM_153612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 6 publications found

Genes affected

HS3ST5 (HGNC:19419): (heparan sulfate-glucosamine 3-sulfotransferase 5) HS3ST5 belongs to a group of heparan sulfate 3-O-sulfotransferases (EC 2.8.2.23) that transfer sulfate from 3-prime-phosphoadenosine 5-prime phosphosulfate (PAPS) to heparan sulfate and heparin (Mochizuki et al., 2003 [PubMed 12740361]).[supplied by OMIM, Mar 2008]

HDAC2-AS2 (HGNC:43590): (HDAC2 and HS3ST5 antisense RNA 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153612.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HS3ST5	NM_153612.4	MANE Select	c.-145+1768C>T		intron	N/A	NP_705840.2
	HS3ST5	NM_001387039.1		c.-33+1768C>T		intron	N/A	NP_001373968.1
	HS3ST5	NM_001387040.1		c.-33+115378C>T		intron	N/A	NP_001373969.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HS3ST5	ENST00000312719.10	TSL:2 MANE Select	c.-145+1768C>T		intron	N/A	ENSP00000427888.1
	HDAC2-AS2	ENST00000519104.5	TSL:1	n.1658-8813G>A		intron	N/A
	HS3ST5	ENST00000900060.1		c.-238+1768C>T		intron	N/A	ENSP00000570119.1

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66743 AN: 151546 Hom.: 14787 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.440 AC: 66773 AN: 151664 Hom.: 14789 Cov.: 32 AF XY: 0.438 AC XY: 32454 AN XY: 74110

African (AFR) AF: 0.456 AC: 18896 AN: 41430

American (AMR) AF: 0.392 AC: 5983 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1598 AN: 3456

East Asian (EAS) AF: 0.462 AC: 2386 AN: 5162

South Asian (SAS) AF: 0.275 AC: 1327 AN: 4822

European-Finnish (FIN) AF: 0.486 AC: 5122 AN: 10548

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29845 AN: 67696

Other (OTH) AF: 0.428 AC: 900 AN: 2104

Alfa AF: 0.438 Hom.: 4869

Bravo AF: 0.438

Asia WGS AF: 0.372 AC: 1290 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.8
DANN	Benign	0.40
PhyloP100		1.1
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: rs9488343; hg19: chr6-114547981;