Genetic Variant NM_015368.4:c.-213_-204dupCCGCCCCGCC (chr11-94129088-T-TCCCGCCCCGC) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2

The NM_015368.4(PANX1):c.-213_-204dupCCGCCCCGCC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.012 ( 43 hom., cov: 0)

Exomes 𝑓: 0.0012 ( 2 hom. )

Consequence

PANX1
NM_015368.4 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.143

Publications

1 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 -8 ACMG points.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0122 (1828/149890) while in subpopulation AFR AF = 0.0414 (1696/40970). AF 95% confidence interval is 0.0398. There are 43 homozygotes in GnomAd4. There are 861 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.

BS2

High AC in GnomAd4 at 1828 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PANX1	NM_015368.4 link	c.-213_-204dupCCGCCCCGCC		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.-213_-204dupCCGCCCCGCC		5_prime_UTR_variant	Exon 1 of 5	1	NM_015368.4	ENSP00000227638.3		Q96RD7-1
PANX1	ENST00000436171.2 link	c.-213_-204dupCCGCCCCGCC		5_prime_UTR_variant	Exon 1 of 5	1		ENSP00000411461.2		Q96RD7-2

Frequencies

GnomAD3 genomes

AF:

0.0122

AC:

1827

AN:

149788

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0415

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00607

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00323

Gnomad NFE

AF:

0.000149

Gnomad OTH

AF:

0.0141

GnomAD4 exome

AF:

0.00116

AC:

302

AN:

259336

Hom.:

Cov.:

AF XY:

0.00104

AC XY:

140

AN XY:

135048

show subpopulations

African (AFR)

AF:

0.0343

AC:

209

AN:

6102

American (AMR)

AF:

0.00339

AC:

AN:

7082

Ashkenazi Jewish (ASJ)

AF:

0.000115

AC:

AN:

8698

East Asian (EAS)

AF:

0.00

AC:

AN:

19774

South Asian (SAS)

AF:

0.0000622

AC:

AN:

16088

European-Finnish (FIN)

AF:

0.00

AC:

AN:

20634

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1314

European-Non Finnish (NFE)

AF:

0.000141

AC:

AN:

163316

Other (OTH)

AF:

0.00269

AC:

AN:

16328

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0122

AC:

1828

AN:

149890

Hom.:

Cov.:

AF XY:

0.0118

AC XY:

861

AN XY:

73098

show subpopulations

African (AFR)

AF:

0.0414

AC:

1696

AN:

40970

American (AMR)

AF:

0.00606

AC:

AN:

15170

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3446

East Asian (EAS)

AF:

0.00

AC:

AN:

4900

South Asian (SAS)

AF:

0.00

AC:

AN:

4734

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10370

Middle Eastern (MID)

AF:

0.00347

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.000149

AC:

AN:

67056

Other (OTH)

AF:

0.0140

AC:

AN:

2076

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

160

239

319

399

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

773

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.14

Mutation Taster

=300/0

polymorphism

(source)

Splicing

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

Publications

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NM_015368.4:c.-213_-204dupCCGCCCCGCC

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