chr11-94129088-T-TCCCGCCCCGC

Variant names:

• chr11-94129088-T-TCCCGCCCCGC
• rs72253125
• NM_015368.4:c.-213_-204dupCCGCCCCGCC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143

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]

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• 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	c.-213_-204dupCCGCCCCGCC		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	c.-213_-204dupCCGCCCCGCC		5_prime_UTR_variant	Exon 1 of 5	1	NM_015368.4	ENSP00000227638.3
PANX1	ENST00000436171	c.-213_-204dupCCGCCCCGCC		5_prime_UTR_variant	Exon 1 of 5	1		ENSP00000411461.2

Frequencies

GnomAD3 genomes AF: 0.0122 AC: 1827 AN: 149788 Hom.: 43 Cov.: 0

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.: 2 Cov.: 0 AF XY: 0.00104 AC XY: 140 AN XY: 135048

Gnomad4 AFR exome AF: 0.0343

Gnomad4 AMR exome AF: 0.00339

Gnomad4 ASJ exome AF: 0.000115

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000622

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000141

Gnomad4 OTH exome AF: 0.00269

GnomAD4 genome AF: 0.0122 AC: 1828 AN: 149890 Hom.: 43 Cov.: 0 AF XY: 0.0118 AC XY: 861 AN XY: 73098

Gnomad4 AFR AF: 0.0414

Gnomad4 AMR AF: 0.00606

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000149

Gnomad4 OTH AF: 0.0140

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72253125; hg19: chr11-93862254;