rs1046805

chr11-94181285-G-Achr11-94181285-G-Cchr11-94181285-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015368.4(PANX1):c.*416G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 165,214 control chromosomes in the GnomAD database, including 38,954 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 0.69 (36051 hom., cov: 32)
  • Exomes 𝑓: 0.67 (2903 hom.)
• Consequence: PANX1 NM_015368.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PANX1	NM_015368.4	c.*416G>A		3_prime_UTR_variant	5/5	ENST00000227638.8
PANX1	XM_011542734.3	c.*416G>A		3_prime_UTR_variant	6/6
PANX1	XM_047426702.1	c.*416G>A		3_prime_UTR_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PANX1	ENST00000227638.8	c.*416G>A		3_prime_UTR_variant	5/5	1	NM_015368.4	P3
PANX1	ENST00000436171.2	c.*416G>A		3_prime_UTR_variant	5/5	1		A1

Frequencies

GnomAD3 genomes AF: 0.685 AC: 104170 AN: 152006 Hom.: 36023 Cov.: 32

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.638

GnomAD4 exome AF: 0.665 AC: 8707 AN: 13090 Hom.: 2903 Cov.: 0 AF XY: 0.668 AC XY: 4516 AN XY: 6760

Gnomad4 AFR exome AF: 0.778

Gnomad4 AMR exome AF: 0.589

Gnomad4 ASJ exome AF: 0.639

Gnomad4 EAS exome AF: 0.707

Gnomad4 SAS exome AF: 0.799

Gnomad4 FIN exome AF: 0.616

Gnomad4 NFE exome AF: 0.657

Gnomad4 OTH exome AF: 0.668

GnomAD4 genome AF: 0.685 AC: 104239 AN: 152124 Hom.: 36051 Cov.: 32 AF XY: 0.686 AC XY: 51014 AN XY: 74348

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.632

Alfa AF: 0.644 Hom.: 32204

Bravo AF: 0.677

Asia WGS AF: 0.727 AC: 2530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.7
Dann	Benign	0.32

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

LitVar

Other links and lift over

dbSNP: rs1046805; hg19: chr11-93914451;