chr11-94128854-C-T

Position:

• chr11-94128854-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_015368.4(PANX1):​c.-459C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,560 control chromosomes in the GnomAD database, including 19,733 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.51 (19674 hom., cov: 34)
  • Exomes 𝑓: 0.47 (59 hom.)
• Consequence: PANX1 NM_015368.4 5_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.323

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BP6: Variant 11-94128854-C-T is Benign according to our data. Variant chr11-94128854-C-T is described in ClinVar as [Benign]. Clinvar id is 1228505.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PANX1	NM_015368.4	c.-459C>T		5_prime_UTR_variant	1/5	ENST00000227638.8	NP_056183.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PANX1	ENST00000227638.8	c.-459C>T		5_prime_UTR_variant	1/5	1	NM_015368.4	ENSP00000227638.3

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76895 AN: 152004 Hom.: 19659 Cov.: 34

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.549

GnomAD4 exome AF: 0.466 AC: 204 AN: 438 Hom.: 59 AF XY: 0.466 AC XY: 110 AN XY: 236

Gnomad4 AFR exome AF: 0.542

Gnomad4 AMR exome AF: 0.583

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.286

Gnomad4 SAS exome AF: 0.600

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.455

Gnomad4 OTH exome AF: 0.450

GnomAD4 genome AF: 0.506 AC: 76957 AN: 152122 Hom.: 19674 Cov.: 34 AF XY: 0.509 AC XY: 37882 AN XY: 74372

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.549

Alfa AF: 0.502 Hom.: 3196

Bravo AF: 0.511

Asia WGS AF: 0.457 AC: 1594 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	15
DANN	Uncertain	0.98

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4753126; hg19: chr11-93862020; COSMIC: COSV57134697;