Genetic Variant PANX1:c.-208_-204delCCGCC (chr11-94129088-TCCCGC-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_015368.4(PANX1):c.-208_-204delCCGCC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 408,236 control chromosomes in the GnomAD database, including 76,765 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.62 ( 29036 hom., cov: 0)

Exomes 𝑓: 0.60 ( 47729 hom. )

Consequence

PANX1
NM_015368.4 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.929

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 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 11-94129088-TCCCGC-T is Benign according to our data. Variant chr11-94129088-TCCCGC-T is described in ClinVar as [Benign]. Clinvar id is 1271612.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PANX1	NM_015368.4 link	c.-208_-204delCCGCC		5_prime_UTR_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
PANX1	ENST00000227638.8 link	c.-208_-204delCCGCC		5_prime_UTR_variant	Exon 1 of 5	1	NM_015368.4	ENSP00000227638.3		Q96RD7-1
PANX1	ENST00000436171.2 link	c.-208_-204delCCGCC		5_prime_UTR_variant	Exon 1 of 5	1		ENSP00000411461.2		Q96RD7-2

Frequencies

GnomAD3 genomes

AF:

0.621

AC:

92983

AN:

149656

Hom.:

29007

Cov.:

show subpopulations

Gnomad AFR

AF:

0.596

Gnomad AMI

AF:

0.631

Gnomad AMR

AF:

0.742

Gnomad ASJ

AF:

0.705

Gnomad EAS

AF:

0.491

Gnomad SAS

AF:

0.525

Gnomad FIN

AF:

0.679

Gnomad MID

AF:

0.613

Gnomad NFE

AF:

0.612

Gnomad OTH

AF:

0.656

GnomAD4 exome

AF:

0.598

AC:

154525

AN:

258478

Hom.:

47729

AF XY:

0.594

AC XY:

79999

AN XY:

134606

show subpopulations

African (AFR)

AF:

0.579

AC:

3526

AN:

6094

American (AMR)

AF:

0.756

AC:

5341

AN:

7062

Ashkenazi Jewish (ASJ)

AF:

0.688

AC:

5972

AN:

8676

East Asian (EAS)

AF:

0.527

AC:

10376

AN:

19696

South Asian (SAS)

AF:

0.502

AC:

8047

AN:

16028

European-Finnish (FIN)

AF:

0.643

AC:

13215

AN:

20554

Middle Eastern (MID)

AF:

0.666

AC:

872

AN:

1310

European-Non Finnish (NFE)

AF:

0.597

AC:

97174

AN:

162770

Other (OTH)

AF:

0.614

AC:

10002

AN:

16288

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

2738

5477

8215

10954

13692

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.621

AC:

93058

AN:

149758

Hom.:

29036

Cov.:

AF XY:

0.623

AC XY:

45481

AN XY:

73038

show subpopulations

African (AFR)

AF:

0.596

AC:

24382

AN:

40934

American (AMR)

AF:

0.742

AC:

11254

AN:

15158

Ashkenazi Jewish (ASJ)

AF:

0.705

AC:

2426

AN:

3442

East Asian (EAS)

AF:

0.492

AC:

2406

AN:

4894

South Asian (SAS)

AF:

0.526

AC:

2489

AN:

4732

European-Finnish (FIN)

AF:

0.679

AC:

7025

AN:

10350

Middle Eastern (MID)

AF:

0.597

AC:

172

AN:

288

European-Non Finnish (NFE)

AF:

0.612

AC:

40991

AN:

67006

Other (OTH)

AF:

0.655

AC:

1359

AN:

2076

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

1668

3335

5003

6670

8338

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.316

Hom.:

773

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jun 21, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.93

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

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

Publications

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11-94129088-TCCCGC-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over