11-94178566-A-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_015368.4(PANX1):c.519A>G(p.Pro173=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,674 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Consequence
PANX1
NM_015368.4 synonymous
NM_015368.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.96
Genes affected
PANX1 (HGNC:8599): (pannexin 1) The protein encoded by this gene belongs to the innexin family. Innexin family members are the structural components of gap junctions. This protein and pannexin 2 are abundantly expressed in central nerve system (CNS) and are coexpressed in various neuronal populations. Studies in Xenopus oocytes suggest that this protein alone and in combination with pannexin 2 may form cell type-specific gap junctions with distinct properties. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 11-94178566-A-G is Benign according to our data. Variant chr11-94178566-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3039980.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.96 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PANX1 | NM_015368.4 | c.519A>G | p.Pro173= | synonymous_variant | 3/5 | ENST00000227638.8 | |
PANX1 | XM_011542734.3 | c.93A>G | p.Pro31= | synonymous_variant | 4/6 | ||
PANX1 | XM_047426702.1 | c.93A>G | p.Pro31= | synonymous_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PANX1 | ENST00000227638.8 | c.519A>G | p.Pro173= | synonymous_variant | 3/5 | 1 | NM_015368.4 | P3 | |
PANX1 | ENST00000436171.2 | c.519A>G | p.Pro173= | synonymous_variant | 3/5 | 1 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250940Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135604
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GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461674Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727132
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GnomAD4 genome ? Cov.: 32
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
PANX1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 10, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
Calibrated prediction
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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