Variant chr14-70977099-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_014982.3(PCNX1):c.762T>G(p.Ser254=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0119 in 1,614,182 control chromosomes in the GnomAD database, including 158 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0090 ( 10 hom., cov: 31)

Exomes 𝑓: 0.012 ( 148 hom. )

Consequence

PCNX1
NM_014982.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.130

Variant links:

Genes affected

PCNX1 (HGNC:19740): (pecanex 1) This gene encodes an evolutionarily conserved transmembrane protein similar to the pecanex protein in Drosophila. The fly protein is a component of the Notch signaling pathway, which functions in several developmental processes. [provided by RefSeq, Jul 2016]

PCNX1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 14-70977099-T-G is Benign according to our data. Variant chr14-70977099-T-G is described in ClinVar as [Benign]. Clinvar id is 2644351.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.13 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 10 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCNX1	NM_014982.3 linkuse as main transcript	c.762T>G	p.Ser254=	synonymous_variant	6/36	ENST00000304743.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCNX1	ENST00000304743.7 linkuse as main transcript	c.762T>G	p.Ser254=	synonymous_variant	6/36	1	NM_014982.3	P4	Q96RV3-1

Frequencies

GnomAD3 genomes

AF:

0.00898

AC:

1367

AN:

152190

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00198

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.00393

Gnomad ASJ

AF:

0.00288

Gnomad EAS

AF:

0.00655

Gnomad SAS

AF:

0.00849

Gnomad FIN

AF:

0.0254

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0124

Gnomad OTH

AF:

0.00766

GnomAD3 exomes

AF:

0.00981

AC:

2466

AN:

251438

Hom.:

AF XY:

0.0100

AC XY:

1364

AN XY:

135898

show subpopulations

Gnomad AFR exome

AF:

0.00172

Gnomad AMR exome

AF:

0.00382

Gnomad ASJ exome

AF:

0.00318

Gnomad EAS exome

AF:

0.00169

Gnomad SAS exome

AF:

0.00604

Gnomad FIN exome

AF:

0.0254

Gnomad NFE exome

AF:

0.0127

Gnomad OTH exome

AF:

0.0103

GnomAD4 exome

AF:

0.0122

AC:

17804

AN:

1461874

Hom.:

148

Cov.:

AF XY:

0.0119

AC XY:

8684

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.00140

Gnomad4 AMR exome

AF:

0.00364

Gnomad4 ASJ exome

AF:

0.00325

Gnomad4 EAS exome

AF:

0.0141

Gnomad4 SAS exome

AF:

0.00574

Gnomad4 FIN exome

AF:

0.0256

Gnomad4 NFE exome

AF:

0.0130

Gnomad4 OTH exome

AF:

0.0111

GnomAD4 genome

AF:

0.00898

AC:

1367

AN:

152308

Hom.:

Cov.:

AF XY:

0.00954

AC XY:

710

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.00197

Gnomad4 AMR

AF:

0.00392

Gnomad4 ASJ

AF:

0.00288

Gnomad4 EAS

AF:

0.00656

Gnomad4 SAS

AF:

0.00849

Gnomad4 FIN

AF:

0.0254

Gnomad4 NFE

AF:

0.0124

Gnomad4 OTH

AF:

0.00758

Alfa

AF:

0.0105

Hom.:

Bravo

AF:

0.00684

Asia WGS

AF:

0.00549

AC:

AN:

3478

EpiCase

AF:

0.0121

EpiControl

AF:

0.00948

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

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

PCNX1: BP4, BP7, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

7.9

DANN

Benign

0.77

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