17-13496169-AT-ATT

Variant names:

• chr17-13496169-A-AT
• rs67951062
• NM_006042.3:c.*27dupA

Variant summary

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

The NM_006042.3(HS3ST3A1):​c.*27dupA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 1,422,978 control chromosomes in the GnomAD database, including 53,840 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.38 (13079 hom., cov: 0)
  • Exomes 𝑓: 0.29 (40761 hom.)
• Consequence: HS3ST3A1 NM_006042.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757
• 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 (AFR) allele frequency at 95% confidence interval = 0.641 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HS3ST3A1	NM_006042.3	MANE Select	c.*27dupA		3_prime_UTR	Exon 2 of 2	NP_006033.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HS3ST3A1	ENST00000284110.2	TSL:1 MANE Select	c.*27dupA		3_prime_UTR	Exon 2 of 2	ENSP00000284110.1
	HS3ST3A1	ENST00000578576.1	TSL:3	c.*27dupA		splice_region	Exon 2 of 2	ENSP00000462696.1
	HS3ST3A1	ENST00000578576.1	TSL:3	c.*27dupA		3_prime_UTR	Exon 2 of 2	ENSP00000462696.1

Frequencies

GnomAD3 genomes AF: 0.383 AC: 57762 AN: 150880 Hom.: 13059 Cov.: 0

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.397

GnomAD2 exomes AF: 0.320 AC: 49649 AN: 155092 AF XY: 0.318

Gnomad AFR exome AF: 0.621

Gnomad AMR exome AF: 0.299

Gnomad ASJ exome AF: 0.359

Gnomad EAS exome AF: 0.214

Gnomad FIN exome AF: 0.253

Gnomad NFE exome AF: 0.316

Gnomad OTH exome AF: 0.332

GnomAD4 exome AF: 0.290 AC: 369420 AN: 1271994 Hom.: 40761 Cov.: 35 AF XY: 0.289 AC XY: 181266 AN XY: 626856

African (AFR) AF: 0.615 AC: 16217 AN: 26378

American (AMR) AF: 0.278 AC: 7420 AN: 26734

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 7184 AN: 21008

East Asian (EAS) AF: 0.202 AC: 6748 AN: 33482

South Asian (SAS) AF: 0.271 AC: 17294 AN: 63722

European-Finnish (FIN) AF: 0.240 AC: 11531 AN: 48142

Middle Eastern (MID) AF: 0.414 AC: 2001 AN: 4834

European-Non Finnish (NFE) AF: 0.286 AC: 284809 AN: 995594

Other (OTH) AF: 0.311 AC: 16216 AN: 52100

GnomAD4 genome AF: 0.383 AC: 57826 AN: 150984 Hom.: 13079 Cov.: 0 AF XY: 0.374 AC XY: 27543 AN XY: 73708

African (AFR) AF: 0.648 AC: 26678 AN: 41194

American (AMR) AF: 0.304 AC: 4606 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1170 AN: 3464

East Asian (EAS) AF: 0.178 AC: 910 AN: 5114

South Asian (SAS) AF: 0.244 AC: 1171 AN: 4800

European-Finnish (FIN) AF: 0.238 AC: 2432 AN: 10226

Middle Eastern (MID) AF: 0.497 AC: 144 AN: 290

European-Non Finnish (NFE) AF: 0.290 AC: 19633 AN: 67728

Other (OTH) AF: 0.396 AC: 827 AN: 2086

Alfa AF: 0.225 Hom.: 365

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.76
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: rs67951062; hg19: chr17-13399486;