Variant rs12801636 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032223.4(PCNX3):c.2512-83G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 1,591,746 control chromosomes in the GnomAD database, including 49,883 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.25 ( 5247 hom., cov: 33)

Exomes 𝑓: 0.24 ( 44636 hom. )

Consequence

PCNX3
NM_032223.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.428

Variant links:

Genes affected

PCNX3 (HGNC:18760): (pecanex 3) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

PCNX3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PCNX3	NM_032223.4 linkuse as main transcript	c.2512-83G>A		intron_variant		ENST00000355703.4	NP_115599.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCNX3	ENST00000355703.4 linkuse as main transcript	c.2512-83G>A		intron_variant		5	NM_032223.4	ENSP00000347931	P1	Q9H6A9-1

Frequencies

GnomAD3 genomes

AF:

0.254

AC:

38667

AN:

152062

Hom.:

5232

Cov.:

show subpopulations

Gnomad AFR

AF:

0.259

Gnomad AMI

AF:

0.189

Gnomad AMR

AF:

0.388

Gnomad ASJ

AF:

0.213

Gnomad EAS

AF:

0.415

Gnomad SAS

AF:

0.261

Gnomad FIN

AF:

0.196

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.221

Gnomad OTH

AF:

0.237

GnomAD4 exome

AF:

0.241

AC:

346701

AN:

1439564

Hom.:

44636

Cov.:

AF XY:

0.240

AC XY:

171825

AN XY:

717338

show subpopulations

Gnomad4 AFR exome

AF:

0.257

Gnomad4 AMR exome

AF:

0.473

Gnomad4 ASJ exome

AF:

0.202

Gnomad4 EAS exome

AF:

0.472

Gnomad4 SAS exome

AF:

0.248

Gnomad4 FIN exome

AF:

0.205

Gnomad4 NFE exome

AF:

0.224

Gnomad4 OTH exome

AF:

0.253

GnomAD4 genome

AF:

0.254

AC:

38717

AN:

152182

Hom.:

5247

Cov.:

AF XY:

0.260

AC XY:

19313

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.259

Gnomad4 AMR

AF:

0.389

Gnomad4 ASJ

AF:

0.213

Gnomad4 EAS

AF:

0.415

Gnomad4 SAS

AF:

0.261

Gnomad4 FIN

AF:

0.196

Gnomad4 NFE

AF:

0.221

Gnomad4 OTH

AF:

0.238

Alfa

AF:

0.238

Hom.:

8481

Bravo

AF:

0.271

Asia WGS

AF:

0.368

AC:

1278

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

6.8

DANN

Benign

0.83

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.11

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over