rs5771206
Positions:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_052839.4(PANX2):āc.1665A>Cā(p.Leu555=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
Exomes š: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PANX2
NM_052839.4 synonymous
NM_052839.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.638
Genes affected
PANX2 (HGNC:8600): (pannexin 2) 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 1 are abundantly expressed in central nervous system (CNS) and are coexpressed in various neuronal populations. Studies in Xenopus oocytes suggest that this protein alone and in combination with pannexin 1 may form cell type-specific gap junctions with distinct properties. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP7
Synonymous conserved (PhyloP=0.638 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PANX2 | NM_052839.4 | c.1665A>C | p.Leu555= | synonymous_variant | 2/3 | ENST00000395842.3 | NP_443071.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PANX2 | ENST00000395842.3 | c.1665A>C | p.Leu555= | synonymous_variant | 2/3 | 2 | NM_052839.4 | ENSP00000379183 | P2 | |
PANX2 | ENST00000159647.9 | c.1665A>C | p.Leu555= | synonymous_variant | 2/4 | 1 | ENSP00000159647 | A2 | ||
PANX2 | ENST00000402472.2 | c.*1452A>C | 3_prime_UTR_variant, NMD_transcript_variant | 3/5 | 2 | ENSP00000384148 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 genomes
Cov.:
34
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1298664Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 636476
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1298664
Hom.:
Cov.:
36
AF XY:
AC XY:
0
AN XY:
636476
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 34
GnomAD4 genome
Cov.:
34
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
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