rs8047014
Variant names:
Your query was ambiguous. Multiple possible variants found:
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
XM_047434045.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.308
Publications
21 publications found
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 |
---|---|---|---|---|---|---|---|---|
HAS3 | XM_047434045.1 | c.-123-4519C>A | intron_variant | Intron 2 of 5 | XP_047290001.1 | |||
HAS3 | XM_047434046.1 | c.-124+1480C>A | intron_variant | Intron 2 of 5 | XP_047290002.1 | |||
HAS3 | XM_047434047.1 | c.-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: 88520AN: 151728Hom.: 26012 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
88520
AN:
151728
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.583 AC: 88575AN: 151844Hom.: 26031 Cov.: 31 AF XY: 0.580 AC XY: 43033AN XY: 74200 show subpopulations
GnomAD4 genome
AF:
AC:
88575
AN:
151844
Hom.:
Cov.:
31
AF XY:
AC XY:
43033
AN XY:
74200
show subpopulations
African (AFR)
AF:
AC:
24689
AN:
41406
American (AMR)
AF:
AC:
9545
AN:
15224
Ashkenazi Jewish (ASJ)
AF:
AC:
2207
AN:
3464
East Asian (EAS)
AF:
AC:
3462
AN:
5152
South Asian (SAS)
AF:
AC:
2504
AN:
4820
European-Finnish (FIN)
AF:
AC:
5083
AN:
10548
Middle Eastern (MID)
AF:
AC:
171
AN:
292
European-Non Finnish (NFE)
AF:
AC:
39321
AN:
67916
Other (OTH)
AF:
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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2026
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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