11-94129088-TCCCGC-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_015368.4(PANX1):c.-208_-204del 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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.929

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 -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/exons	MANE	UniProt
PANX1	NM_015368.4	c.-208_-204del		5_prime_UTR_variant	1/5	ENST00000227638.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PANX1	ENST00000227638.8	c.-208_-204del		5_prime_UTR_variant	1/5	1	NM_015368.4	P3
PANX1	ENST00000436171.2	c.-208_-204del		5_prime_UTR_variant	1/5	1		A1

Frequencies

GnomAD3 genomes AF: 0.621 AC: 92983 AN: 149656 Hom.: 29007 Cov.: 0

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

Gnomad4 AFR exome AF: 0.579

Gnomad4 AMR exome AF: 0.756

Gnomad4 ASJ exome AF: 0.688

Gnomad4 EAS exome AF: 0.527

Gnomad4 SAS exome AF: 0.502

Gnomad4 FIN exome AF: 0.643

Gnomad4 NFE exome AF: 0.597

Gnomad4 OTH exome AF: 0.614

GnomAD4 genome AF: 0.621 AC: 93058 AN: 149758 Hom.: 29036 Cov.: 0 AF XY: 0.623 AC XY: 45481 AN XY: 73038

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.679

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.655

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 21, 2021

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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;