11-94129088-TCCCGCCCCGCCCCGC-TCCCGCCCCGCCCCGCCCCGC

Variant names:

• chr11-94129088-T-TCCCGC
• rs72253125
• NM_015368.4:c.-208_-204dupCCGCC

Variant summary

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

The NM_015368.4(PANX1):​c.-208_-204dupCCGCC 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 0.00076 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00061 (0 hom.)
• 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 114 AD gene.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.000761 AC: 114 AN: 149800 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000171

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000792

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000611

Gnomad SAS AF: 0.000211

Gnomad FIN AF: 0.00530

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000537

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000613 AC: 159 AN: 259346 Hom.: 0 Cov.: 0 AF XY: 0.000585 AC XY: 79 AN XY: 135056

African (AFR) AF: 0.000491 AC: 3 AN: 6110

American (AMR) AF: 0.000282 AC: 2 AN: 7084

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

East Asian (EAS) AF: 0.000506 AC: 10 AN: 19774

South Asian (SAS) AF: 0.000186 AC: 3 AN: 16088

European-Finnish (FIN) AF: 0.00320 AC: 66 AN: 20632

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

European-Non Finnish (NFE) AF: 0.000349 AC: 57 AN: 163318

Other (OTH) AF: 0.00110 AC: 18 AN: 16328

GnomAD4 genome AF: 0.000760 AC: 114 AN: 149902 Hom.: 0 Cov.: 0 AF XY: 0.000985 AC XY: 72 AN XY: 73100

African (AFR) AF: 0.000171 AC: 7 AN: 40980

American (AMR) AF: 0.000791 AC: 12 AN: 15170

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

East Asian (EAS) AF: 0.000612 AC: 3 AN: 4900

South Asian (SAS) AF: 0.000211 AC: 1 AN: 4734

European-Finnish (FIN) AF: 0.00530 AC: 55 AN: 10370

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 288

European-Non Finnish (NFE) AF: 0.000537 AC: 36 AN: 67056

Other (OTH) AF: 0.00 AC: 0 AN: 2078

Alfa AF: 0.00123 Hom.: 773

Bravo AF: 0.000257

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;