chr17-13601348-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006042.3(HS3ST3A1):​c.-219T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 488,678 control chromosomes in the GnomAD database, including 15,038 homozygotes. 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 0.25 ( 5146 hom., cov: 33)
Exomes 𝑓: 0.23 ( 9892 hom. )

Consequence

HS3ST3A1
NM_006042.3 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.113
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HS3ST3A1NM_006042.3 linkuse as main transcriptc.-219T>C 5_prime_UTR_variant 1/2 ENST00000284110.2 NP_006033.1 Q9Y663
HS3ST3A1XM_017025480.3 linkuse as main transcriptc.-219T>C 5_prime_UTR_variant 1/2 XP_016880969.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HS3ST3A1ENST00000284110.2 linkuse as main transcriptc.-219T>C 5_prime_UTR_variant 1/21 NM_006042.3 ENSP00000284110.1 Q9Y663

Frequencies

GnomAD3 genomes
AF:
0.255
AC:
38690
AN:
151938
Hom.:
5134
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.316
Gnomad AMI
AF:
0.282
Gnomad AMR
AF:
0.191
Gnomad ASJ
AF:
0.223
Gnomad EAS
AF:
0.0843
Gnomad SAS
AF:
0.202
Gnomad FIN
AF:
0.203
Gnomad MID
AF:
0.250
Gnomad NFE
AF:
0.258
Gnomad OTH
AF:
0.244
GnomAD4 exome
AF:
0.235
AC:
78941
AN:
336622
Hom.:
9892
Cov.:
3
AF XY:
0.233
AC XY:
41035
AN XY:
175868
show subpopulations
Gnomad4 AFR exome
AF:
0.310
Gnomad4 AMR exome
AF:
0.168
Gnomad4 ASJ exome
AF:
0.226
Gnomad4 EAS exome
AF:
0.110
Gnomad4 SAS exome
AF:
0.211
Gnomad4 FIN exome
AF:
0.202
Gnomad4 NFE exome
AF:
0.255
Gnomad4 OTH exome
AF:
0.241
GnomAD4 genome
AF:
0.255
AC:
38738
AN:
152056
Hom.:
5146
Cov.:
33
AF XY:
0.247
AC XY:
18350
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.316
Gnomad4 AMR
AF:
0.191
Gnomad4 ASJ
AF:
0.223
Gnomad4 EAS
AF:
0.0845
Gnomad4 SAS
AF:
0.202
Gnomad4 FIN
AF:
0.203
Gnomad4 NFE
AF:
0.258
Gnomad4 OTH
AF:
0.249
Alfa
AF:
0.261
Hom.:
680
Bravo
AF:
0.256
Asia WGS
AF:
0.171
AC:
596
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
9.5
DANN
Benign
0.70

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3744337; hg19: chr17-13504665; API