GeneBe

17-13496169-AT-ATTTTTT

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_006042.3(HS3ST3A1):​c.*23_*27dupAAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000154 in 1,301,210 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000015 ( 0 hom. )

Consequence

HS3ST3A1
NM_006042.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.757

Publications

0 publications found
Variant links:
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]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
HS3ST3A1NM_006042.3 linkc.*23_*27dupAAAAA 3_prime_UTR_variant Exon 2 of 2 ENST00000284110.2 NP_006033.1 Q9Y663
HS3ST3A1XM_011524114.4 linkc.*23_*27dupAAAAA 3_prime_UTR_variant Exon 3 of 3 XP_011522416.1
HS3ST3A1XM_047437228.1 linkc.*23_*27dupAAAAA 3_prime_UTR_variant Exon 2 of 2 XP_047293184.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HS3ST3A1ENST00000284110.2 linkc.*23_*27dupAAAAA 3_prime_UTR_variant Exon 2 of 2 1 NM_006042.3 ENSP00000284110.1 Q9Y663
HS3ST3A1ENST00000578576.1 linkc.*23_*27dupAAAAA splice_region_variant Exon 2 of 2 3 ENSP00000462696.1 J3KSX5
HS3ST3A1ENST00000578576.1 linkc.*23_*27dupAAAAA 3_prime_UTR_variant Exon 2 of 2 3 ENSP00000462696.1 J3KSX5

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000154
AC:
2
AN:
1301210
Hom.:
0
Cov.:
35
AF XY:
0.00000312
AC XY:
2
AN XY:
641384
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
26548
American (AMR)
AF:
0.00
AC:
0
AN:
27990
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
21444
East Asian (EAS)
AF:
0.00
AC:
0
AN:
35056
South Asian (SAS)
AF:
0.00
AC:
0
AN:
65906
European-Finnish (FIN)
AF:
0.0000205
AC:
1
AN:
48818
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4904
European-Non Finnish (NFE)
AF:
9.83e-7
AC:
1
AN:
1017290
Other (OTH)
AF:
0.00
AC:
0
AN:
53254
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
-0.76

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs67951062; hg19: chr17-13399486; API