chr16-69115194-A-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001199280.2(HAS3):c.1590A>G(p.Leu530=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00505 in 1,567,160 control chromosomes in the GnomAD database, including 303 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.026 ( 159 hom., cov: 32)
Exomes 𝑓: 0.0028 ( 144 hom. )
Consequence
HAS3
NM_001199280.2 synonymous
NM_001199280.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.92
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 made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 16-69115194-A-G is Benign according to our data. Variant chr16-69115194-A-G is described in ClinVar as [Benign]. Clinvar id is 781209.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.92 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0852 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HAS3 | NM_001199280.2 | c.1590A>G | p.Leu530= | synonymous_variant | 4/4 | ENST00000569188.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAS3 | ENST00000569188.6 | c.1590A>G | p.Leu530= | synonymous_variant | 4/4 | 2 | NM_001199280.2 | P1 | |
HAS3 | ENST00000306560.1 | c.1590A>G | p.Leu530= | synonymous_variant | 4/4 | 1 | P1 | ||
HAS3 | ENST00000219322.7 | c.738+1652A>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0256 AC: 3888AN: 151946Hom.: 159 Cov.: 32
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GnomAD3 exomes AF: 0.00783 AC: 1663AN: 212490Hom.: 59 AF XY: 0.00567 AC XY: 642AN XY: 113310
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GnomAD4 exome AF: 0.00284 AC: 4020AN: 1415096Hom.: 144 Cov.: 34 AF XY: 0.00246 AC XY: 1721AN XY: 699078
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GnomAD4 genome ? AF: 0.0256 AC: 3893AN: 152064Hom.: 159 Cov.: 32 AF XY: 0.0253 AC XY: 1880AN XY: 74310
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at