Genetic Variant PANX1:c.*416G>A (chr11-94181285-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.03

Publications

10 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)

PANX1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015368.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PANX1	NM_015368.4	MANE Select	c.*416G>A		3_prime_UTR	Exon 5 of 5	NP_056183.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PANX1	ENST00000227638.8	TSL:1 MANE Select	c.*416G>A	3_prime_UTR	Exon 5 of 5	ENSP00000227638.3	Q96RD7-1
PANX1	ENST00000436171.2	TSL:1	c.*416G>A	3_prime_UTR	Exon 5 of 5	ENSP00000411461.2	Q96RD7-2
PANX1	ENST00000931248.1		c.*416G>A	3_prime_UTR	Exon 5 of 5	ENSP00000601307.1

Frequencies

GnomAD3 genomes

AF:

0.685

AC:

104170

AN:

152006

Hom.:

36023

Cov.:

show subpopulations

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.:

AF XY:

0.668

AC XY:

4516

AN XY:

6760

show subpopulations

African (AFR)

AF:

0.778

AC:

302

AN:

388

American (AMR)

AF:

0.589

AC:

981

AN:

1666

Ashkenazi Jewish (ASJ)

AF:

0.639

AC:

244

AN:

382

East Asian (EAS)

AF:

0.707

AC:

677

AN:

958

South Asian (SAS)

AF:

0.799

AC:

775

AN:

970

European-Finnish (FIN)

AF:

0.616

AC:

218

AN:

354

Middle Eastern (MID)

AF:

0.650

AC:

AN:

European-Non Finnish (NFE)

AF:

0.657

AC:

5022

AN:

7640

Other (OTH)

AF:

0.668

AC:

462

AN:

692

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

147

294

440

587

734

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

164

246

328

410

<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

AF:

0.685

AC:

104239

AN:

152124

Hom.:

36051

Cov.:

AF XY:

0.686

AC XY:

51014

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.772

AC:

32038

AN:

41498

American (AMR)

AF:

0.588

AC:

8993

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.626

AC:

2171

AN:

3470

East Asian (EAS)

AF:

0.723

AC:

3742

AN:

5174

South Asian (SAS)

AF:

0.813

AC:

3919

AN:

4822

European-Finnish (FIN)

AF:

0.652

AC:

6884

AN:

10564

Middle Eastern (MID)

AF:

0.656

AC:

193

AN:

294

European-Non Finnish (NFE)

AF:

0.650

AC:

44231

AN:

67998

Other (OTH)

AF:

0.632

AC:

1332

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1695

3390

5084

6779

8474

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

820

1640

2460

3280

4100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.649

Hom.:

42703

Bravo

AF:

0.677

Asia WGS

AF:

0.727

AC:

2530

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.7

(source)

DANN

Benign

0.32

PhyloP100

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over