rs78863672

chr17-13601920-C-Achr17-13601920-C-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_006042.3(HS3ST3A1):c.-791G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.52 (1791 hom., cov: 0)
  • Exomes 𝑓: 0.011 (1 hom.)
  • Failed GnomAD Quality Control
• Consequence: HS3ST3A1 NM_006042.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

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 Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HS3ST3A1	NM_006042.3	c.-791G>T		5_prime_UTR_variant	1/2	ENST00000284110.2
HS3ST3A1	XM_017025480.3	c.-791G>T		5_prime_UTR_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HS3ST3A1	ENST00000284110.2	c.-791G>T		5_prime_UTR_variant	1/2	1	NM_006042.3	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 16026 AN: 30916 Hom.: 1789 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.450

GnomAD4 exome AF: 0.0110 AC: 10 AN: 912 Hom.: 1 Cov.: 0 AF XY: 0.0117 AC XY: 8 AN XY: 684

Gnomad4 AFR exome AF: 0.167

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0113

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.518 AC: 16050 AN: 30956 Hom.: 1791 Cov.: 0 AF XY: 0.520 AC XY: 7701 AN XY: 14814

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.452

Alfa AF: 0.0216 Hom.: 31

Bravo AF: 0.117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
Cadd	Benign	13
Dann	Benign	0.73

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: rs78863672; hg19: chr17-13505237;