rs58718148

Variant names:

• chr17-13601926-TG-T
• rs58718148
• NM_006042.3:c.-798delC

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_006042.3(HS3ST3A1):​c.-798delC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.99 (74673 hom., cov: 0)
  • Exomes 𝑓: 1.0 (286 hom.)
• Consequence: HS3ST3A1 NM_006042.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 1 publications found

Genes affected

HS3ST3A1 (HGNC:5196): (heparan sulfate-glucosamine 3-sulfotransferase 3A1) Heparan sulfate biosynthetic enzymes are key components in generating a myriad of distinct heparan sulfate fine structures that carry out multiple biologic activities. The enzyme encoded by this gene is a member of the heparan sulfate biosynthetic enzyme family. It is a type II integral membrane protein and possesses heparan sulfate glucosaminyl 3-O-sulfotransferase activity. The sulfotransferase domain of this enzyme is highly similar to the same domain of heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3B1, and these two enzymes sulfate an identical disaccharide. This gene is widely expressed, with the most abundant expression in liver and placenta. [provided by RefSeq, Dec 2014]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006042.3. 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
	HS3ST3A1	NM_006042.3	MANE Select	c.-798delC		5_prime_UTR	Exon 1 of 2	NP_006033.1	Q9Y663

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HS3ST3A1	ENST00000284110.2	TSL:1 MANE Select	c.-798delC		5_prime_UTR	Exon 1 of 2	ENSP00000284110.1	Q9Y663

Frequencies

GnomAD3 genomes AF: 0.990 AC: 150686 AN: 152170 Hom.: 74617 Cov.: 0

Gnomad AFR AF: 0.981

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.988

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.996

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.939

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.984

GnomAD4 exome AF: 0.998 AC: 573 AN: 574 Hom.: 286 Cov.: 0 AF XY: 1.00 AC XY: 414 AN XY: 414

African (AFR) AF: 1.00 AC: 4 AN: 4

American (AMR) AF: 1.00 AC: 4 AN: 4

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 4 AN: 4

East Asian (EAS) AF: 1.00 AC: 18 AN: 18

South Asian (SAS) AF: 1.00 AC: 20 AN: 20

European-Finnish (FIN) AF: 1.00 AC: 6 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.998 AC: 505 AN: 506

Other (OTH) AF: 1.00 AC: 12 AN: 12

GnomAD4 genome AF: 0.990 AC: 150796 AN: 152278 Hom.: 74673 Cov.: 0 AF XY: 0.991 AC XY: 73751 AN XY: 74458

African (AFR) AF: 0.981 AC: 40783 AN: 41574

American (AMR) AF: 0.988 AC: 15125 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.963 AC: 3343 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5126 AN: 5126

South Asian (SAS) AF: 0.996 AC: 4813 AN: 4832

European-Finnish (FIN) AF: 1.00 AC: 10628 AN: 10628

Middle Eastern (MID) AF: 0.945 AC: 276 AN: 292

European-Non Finnish (NFE) AF: 0.996 AC: 67716 AN: 68022

Other (OTH) AF: 0.984 AC: 2081 AN: 2114

Alfa AF: 0.993 Hom.: 8054

Asia WGS AF: 0.996 AC: 3414 AN: 3426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.19
Mutation Taster		=294/6	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: rs58718148; hg19: chr17-13505243; COSMIC: COSV52377734;