Variant 22-50178377-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_052839.4(PANX2):c.1665A>G(p.Leu555Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 1,448,638 control chromosomes in the GnomAD database, including 297,179 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 0.61 ( 28613 hom., cov: 34)

Exomes 𝑓: 0.64 ( 268566 hom. )

Consequence

PANX2
NM_052839.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.638

Variant links:

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]

PANX2 links:

PANX2 (HGNC:):

PANX2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BP7

Synonymous conserved (PhyloP=0.638 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PANX2	NM_052839.4 linkuse as main transcript	c.1665A>G	p.Leu555Leu	synonymous_variant	2/3	ENST00000395842.3	NP_443071.2	Q96RD6-3B3KTT7Q495U3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
PANX2	ENST00000395842.3 linkuse as main transcript	c.1665A>G	p.Leu555Leu	synonymous_variant	2/3	2	NM_052839.4	ENSP00000379183.2	Q96RD6-3
PANX2	ENST00000159647.9 linkuse as main transcript	c.1665A>G	p.Leu555Leu	synonymous_variant	2/4	1		ENSP00000159647.5	Q96RD6-1
PANX2	ENST00000402472.2 linkuse as main transcript	n.*1452A>G		non_coding_transcript_exon_variant	3/5	2		ENSP00000384148.2	F8W8Y4
PANX2	ENST00000402472.2 linkuse as main transcript	n.*1452A>G		3_prime_UTR_variant	3/5	2		ENSP00000384148.2	F8W8Y4

Frequencies

GnomAD3 genomes

AF:

0.610

AC:

92650

AN:

151910

Hom.:

28591

Cov.:

show subpopulations

Gnomad AFR

AF:

0.549

Gnomad AMI

AF:

0.603

Gnomad AMR

AF:

0.572

Gnomad ASJ

AF:

0.605

Gnomad EAS

AF:

0.497

Gnomad SAS

AF:

0.566

Gnomad FIN

AF:

0.686

Gnomad MID

AF:

0.548

Gnomad NFE

AF:

0.656

Gnomad OTH

AF:

0.603

GnomAD3 exomes

AF:

0.583

AC:

33754

AN:

57908

Hom.:

9917

AF XY:

0.582

AC XY:

19371

AN XY:

33274

show subpopulations

Gnomad AFR exome

AF:

0.496

Gnomad AMR exome

AF:

0.501

Gnomad ASJ exome

AF:

0.605

Gnomad EAS exome

AF:

0.453

Gnomad SAS exome

AF:

0.561

Gnomad FIN exome

AF:

0.638

Gnomad NFE exome

AF:

0.641

Gnomad OTH exome

AF:

0.607

GnomAD4 exome

AF:

0.642

AC:

832378

AN:

1296608

Hom.:

268566

Cov.:

AF XY:

0.639

AC XY:

405775

AN XY:

635444

show subpopulations

Gnomad4 AFR exome

AF:

0.546

Gnomad4 AMR exome

AF:

0.521

Gnomad4 ASJ exome

AF:

0.606

Gnomad4 EAS exome

AF:

0.488

Gnomad4 SAS exome

AF:

0.570

Gnomad4 FIN exome

AF:

0.659

Gnomad4 NFE exome

AF:

0.657

Gnomad4 OTH exome

AF:

0.630

GnomAD4 genome

AF:

0.610

AC:

92722

AN:

152030

Hom.:

28613

Cov.:

AF XY:

0.610

AC XY:

45310

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.549

Gnomad4 AMR

AF:

0.572

Gnomad4 ASJ

AF:

0.605

Gnomad4 EAS

AF:

0.497

Gnomad4 SAS

AF:

0.567

Gnomad4 FIN

AF:

0.686

Gnomad4 NFE

AF:

0.656

Gnomad4 OTH

AF:

0.599

Alfa

AF:

0.621

Hom.:

6439

Bravo

AF:

0.596

Asia WGS

AF:

0.533

AC:

1851

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.0

DANN

Benign

0.68

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over