Variant 11-94153672-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_015368.4(PANX1):c.321+42G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 1,587,884 control chromosomes in the GnomAD database, including 174,536 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.48 ( 17483 hom., cov: 32)

Exomes 𝑓: 0.46 ( 157053 hom. )

Consequence

PANX1
NM_015368.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.859

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 11-94153672-G-C is Benign according to our data. Variant chr11-94153672-G-C is described in ClinVar as [Benign]. Clinvar id is 1244633.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
PANX1	NM_015368.4 linkuse as main transcript	c.321+42G>C	intron_variant	ENST00000227638.8
PANX1	XM_011542734.3 linkuse as main transcript	c.-352+42G>C	intron_variant
PANX1	XM_047426702.1 linkuse as main transcript	c.-248+42G>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PANX1	ENST00000227638.8 linkuse as main transcript	c.321+42G>C		intron_variant		1	NM_015368.4	P3	Q96RD7-1
PANX1	ENST00000436171.2 linkuse as main transcript	c.321+42G>C		intron_variant		1		A1	Q96RD7-2

Frequencies

GnomAD3 genomes

AF:

0.476

AC:

72351

AN:

151918

Hom.:

17455

Cov.:

show subpopulations

Gnomad AFR

AF:

0.482

Gnomad AMI

AF:

0.263

Gnomad AMR

AF:

0.577

Gnomad ASJ

AF:

0.544

Gnomad EAS

AF:

0.401

Gnomad SAS

AF:

0.296

Gnomad FIN

AF:

0.506

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.463

Gnomad OTH

AF:

0.511

GnomAD3 exomes

AF:

0.477

AC:

110639

AN:

231748

Hom.:

27166

AF XY:

0.463

AC XY:

58097

AN XY:

125560

show subpopulations

Gnomad AFR exome

AF:

0.485

Gnomad AMR exome

AF:

0.657

Gnomad ASJ exome

AF:

0.537

Gnomad EAS exome

AF:

0.417

Gnomad SAS exome

AF:

0.312

Gnomad FIN exome

AF:

0.507

Gnomad NFE exome

AF:

0.465

Gnomad OTH exome

AF:

0.475

GnomAD4 exome

AF:

0.464

AC:

666766

AN:

1435846

Hom.:

157053

Cov.:

AF XY:

0.459

AC XY:

327346

AN XY:

713906

show subpopulations

Gnomad4 AFR exome

AF:

0.481

Gnomad4 AMR exome

AF:

0.644

Gnomad4 ASJ exome

AF:

0.537

Gnomad4 EAS exome

AF:

0.428

Gnomad4 SAS exome

AF:

0.307

Gnomad4 FIN exome

AF:

0.496

Gnomad4 NFE exome

AF:

0.468

Gnomad4 OTH exome

AF:

0.463

GnomAD4 genome

AF:

0.476

AC:

72431

AN:

152038

Hom.:

17483

Cov.:

AF XY:

0.477

AC XY:

35432

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.481

Gnomad4 AMR

AF:

0.578

Gnomad4 ASJ

AF:

0.544

Gnomad4 EAS

AF:

0.401

Gnomad4 SAS

AF:

0.296

Gnomad4 FIN

AF:

0.506

Gnomad4 NFE

AF:

0.463

Gnomad4 OTH

AF:

0.516

Alfa

AF:

0.476

Hom.:

3396

Bravo

AF:

0.489

Asia WGS

AF:

0.395

AC:

1376

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

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

-0.83

CADD

Benign

6.0

DANN

Benign

0.59

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over