chr11-94129088-T-TCCCGCCCCGCCCCGC

Variant names:

• chr11-94129088-T-TCCCGCCCCGCCCCGC
• rs72253125
• NM_015368.4:c.-218_-204dupCCGCCCCGCCCCGCC

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_015368.4(PANX1):​c.-218_-204dupCCGCCCCGCCCCGCC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000087 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PANX1 NM_015368.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 1 publications found

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)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BS2: High AC in GnomAd4 at 13 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PANX1	NM_015368.4	c.-218_-204dupCCGCCCCGCCCCGCC		5_prime_UTR_variant	Exon 1 of 5	ENST00000227638.8	NP_056183.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PANX1	ENST00000227638.8	c.-218_-204dupCCGCCCCGCCCCGCC		5_prime_UTR_variant	Exon 1 of 5	1	NM_015368.4	ENSP00000227638.3
PANX1	ENST00000436171.2	c.-218_-204dupCCGCCCCGCCCCGCC		5_prime_UTR_variant	Exon 1 of 5	1		ENSP00000411461.2

Frequencies

GnomAD3 genomes AF: 0.0000868 AC: 13 AN: 149800 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000318

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 259350 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 135058

African (AFR) AF: 0.00 AC: 0 AN: 6110

American (AMR) AF: 0.00 AC: 0 AN: 7084

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8698

East Asian (EAS) AF: 0.00 AC: 0 AN: 19774

South Asian (SAS) AF: 0.00 AC: 0 AN: 16088

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 20634

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1314

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 163318

Other (OTH) AF: 0.00 AC: 0 AN: 16330

GnomAD4 genome AF: 0.0000868 AC: 13 AN: 149800 Hom.: 0 Cov.: 0 AF XY: 0.0000685 AC XY: 5 AN XY: 72980

African (AFR) AF: 0.000318 AC: 13 AN: 40866

American (AMR) AF: 0.00 AC: 0 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3446

East Asian (EAS) AF: 0.00 AC: 0 AN: 4914

South Asian (SAS) AF: 0.00 AC: 0 AN: 4742

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10370

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 310

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67064

Other (OTH) AF: 0.00 AC: 0 AN: 2058

Alfa AF: 0.00 Hom.: 773

Bravo AF: 0.0000982

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs72253125; hg19: chr11-93862254;