17-13496169-AT-A

Position:

• chr17-13496169-AT-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_006042.3(HS3ST3A1):​c.*27del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000248 in 1,452,160 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00029 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00024 (1 hom.)
• Consequence: HS3ST3A1 NM_006042.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HS3ST3A1	NM_006042.3	c.*27del		3_prime_UTR_variant	2/2	ENST00000284110.2
HS3ST3A1	XM_011524114.4	c.*27del		3_prime_UTR_variant	3/3
HS3ST3A1	XM_047437228.1	c.*27del		3_prime_UTR_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HS3ST3A1	ENST00000284110.2	c.*27del		3_prime_UTR_variant	2/2	1	NM_006042.3	P1
HS3ST3A1	ENST00000578576.1	c.*27del		3_prime_UTR_variant	2/2	3

Frequencies

GnomAD3 genomes AF: 0.000291 AC: 44 AN: 150986 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000243

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00683

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000295

Gnomad OTH AF: 0.000483

GnomAD3 exomes AF: 0.000967 AC: 150 AN: 155092 Hom.: 0 AF XY: 0.000891 AC XY: 76 AN XY: 85292

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000117

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0113

Gnomad SAS exome AF: 0.000250

Gnomad FIN exome AF: 0.0000616

Gnomad NFE exome AF: 0.000186

Gnomad OTH exome AF: 0.000270

GnomAD4 exome AF: 0.000243 AC: 316 AN: 1301070 Hom.: 1 Cov.: 35 AF XY: 0.000254 AC XY: 163 AN XY: 641310

Gnomad4 AFR exome AF: 0.0000753

Gnomad4 AMR exome AF: 0.0000715

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00633

Gnomad4 SAS exome AF: 0.000364

Gnomad4 FIN exome AF: 0.0000205

Gnomad4 NFE exome AF: 0.0000442

Gnomad4 OTH exome AF: 0.000357

GnomAD4 genome AF: 0.000291 AC: 44 AN: 151090 Hom.: 0 Cov.: 0 AF XY: 0.000353 AC XY: 26 AN XY: 73758

Gnomad4 AFR AF: 0.0000243

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00684

Gnomad4 SAS AF: 0.00104

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000295

Gnomad4 OTH AF: 0.000478

Alfa AF: 0.000294 Hom.: 365

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: rs67951062; hg19: chr17-13399486;