dbSNP rs1046805: 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PANX1	NM_015368.4 link	c.*416G>A	3_prime_UTR_variant	Exon 5 of 5	ENST00000227638.8	NP_056183.2	Q96RD7-1A0A024R397
PANX1	XM_011542734.3 link	c.*416G>A	3_prime_UTR_variant	Exon 6 of 6		XP_011541036.1
PANX1	XM_047426702.1 link	c.*416G>A	3_prime_UTR_variant	Exon 5 of 5		XP_047282658.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PANX1	ENST00000227638.8 link	c.*416G>A		3_prime_UTR_variant	Exon 5 of 5	1	NM_015368.4	ENSP00000227638.3		Q96RD7-1
PANX1	ENST00000436171.2 link	c.*416G>A		3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000411461.2		Q96RD7-2

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over