GeneBe

chr11-94129327-A-G

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7

The NM_015368.4(PANX1):​c.15A>G​(p.Gln5Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,457,926 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 33)
Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

PANX1
NM_015368.4 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.261

Publications

51 publications found
Variant links:
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]
PANX1 Gene-Disease associations (from GenCC):
  • oocyte maturation defect 7
    Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP7
Synonymous conserved (PhyloP=0.261 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PANX1NM_015368.4 linkc.15A>G p.Gln5Gln synonymous_variant Exon 1 of 5 ENST00000227638.8 NP_056183.2 Q96RD7-1A0A024R397

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PANX1ENST00000227638.8 linkc.15A>G p.Gln5Gln synonymous_variant Exon 1 of 5 1 NM_015368.4 ENSP00000227638.3 Q96RD7-1
PANX1ENST00000436171.2 linkc.15A>G p.Gln5Gln synonymous_variant Exon 1 of 5 1 ENSP00000411461.2 Q96RD7-2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000274
AC:
4
AN:
1457926
Hom.:
0
Cov.:
43
AF XY:
0.00000276
AC XY:
2
AN XY:
724776
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33400
American (AMR)
AF:
0.00
AC:
0
AN:
44560
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
26080
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39470
South Asian (SAS)
AF:
0.0000116
AC:
1
AN:
85976
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53294
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5756
European-Non Finnish (NFE)
AF:
0.00000270
AC:
3
AN:
1109180
Other (OTH)
AF:
0.00
AC:
0
AN:
60210
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.46
CADD
Benign
12
DANN
Benign
0.84
PhyloP100
0.26
PromoterAI
0.035
Neutral

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs1138800; hg19: chr11-93862493; API