rs58718148

chr17-13601926-TG-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_006042.3(HS3ST3A1):c.-798del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.99 in 152,852 control chromosomes in the GnomAD database, including 74,959 homozygotes. 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

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

Verdict is Benign. Variant got -8 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HS3ST3A1	NM_006042.3	c.-798del		5_prime_UTR_variant	1/2	ENST00000284110.2
HS3ST3A1	XM_017025480.3	c.-798del		5_prime_UTR_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HS3ST3A1	ENST00000284110.2	c.-798del		5_prime_UTR_variant	1/2	1	NM_006042.3	P1

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

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 1.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.998

Gnomad4 OTH exome AF: 1.00

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

Gnomad4 AFR AF: 0.981

Gnomad4 AMR AF: 0.988

Gnomad4 ASJ AF: 0.963

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.996

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.996

Gnomad4 OTH AF: 0.984

Alfa AF: 0.993 Hom.: 8054

Asia WGS AF: 0.996 AC: 3414 AN: 3426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs58718148; hg19: chr17-13505243;