rs8047014

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XM_047434045.1(HAS3):​c.-123-4519C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 151,844 control chromosomes in the GnomAD database, including 26,031 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 0.58 ( 26031 hom., cov: 31)

Consequence

HAS3
XM_047434045.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.308

Publications

21 publications found
Variant links:
Genes affected
HAS3 (HGNC:4820): (hyaluronan synthase 3) The protein encoded by this gene is involved in the synthesis of the unbranched glycosaminoglycan hyaluronan, or hyaluronic acid, which is a major constituent of the extracellular matrix. This gene is a member of the NODC/HAS gene family. Compared to the proteins encoded by other members of this gene family, this protein appears to be more of a regulator of hyaluronan synthesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2010]

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
HAS3XM_047434045.1 linkc.-123-4519C>A intron_variant Intron 2 of 5 XP_047290001.1
HAS3XM_047434046.1 linkc.-124+1480C>A intron_variant Intron 2 of 5 XP_047290002.1
HAS3XM_047434047.1 linkc.-104+1480C>A intron_variant Intron 2 of 5 XP_047290003.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.583
AC:
88520
AN:
151728
Hom.:
26012
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.597
Gnomad AMI
AF:
0.387
Gnomad AMR
AF:
0.627
Gnomad ASJ
AF:
0.637
Gnomad EAS
AF:
0.672
Gnomad SAS
AF:
0.518
Gnomad FIN
AF:
0.482
Gnomad MID
AF:
0.592
Gnomad NFE
AF:
0.579
Gnomad OTH
AF:
0.594
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.583
AC:
88575
AN:
151844
Hom.:
26031
Cov.:
31
AF XY:
0.580
AC XY:
43033
AN XY:
74200
show subpopulations
African (AFR)
AF:
0.596
AC:
24689
AN:
41406
American (AMR)
AF:
0.627
AC:
9545
AN:
15224
Ashkenazi Jewish (ASJ)
AF:
0.637
AC:
2207
AN:
3464
East Asian (EAS)
AF:
0.672
AC:
3462
AN:
5152
South Asian (SAS)
AF:
0.520
AC:
2504
AN:
4820
European-Finnish (FIN)
AF:
0.482
AC:
5083
AN:
10548
Middle Eastern (MID)
AF:
0.586
AC:
171
AN:
292
European-Non Finnish (NFE)
AF:
0.579
AC:
39321
AN:
67916
Other (OTH)
AF:
0.588
AC:
1240
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1856
3712
5569
7425
9281
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
738
1476
2214
2952
3690
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.585
Hom.:
86235
Bravo
AF:
0.595
Asia WGS
AF:
0.582
AC:
2026
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
0.92
DANN
Benign
0.72
PhyloP100
-0.31

Splicing

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

Publications

Other links and lift over

dbSNP: rs8047014; hg19: chr16-69135049; API