14-70988600-G-A

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_014982.3(PCNX1):​c.2345G>A​(p.Arg782His) variant causes a missense change. The variant allele was found at a frequency of 0.0037 in 1,614,050 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0023 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0038 ( 16 hom. )

Consequence

PCNX1
NM_014982.3 missense

Scores

2
5
11

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 6.23
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.009532601).
BP6
Variant 14-70988600-G-A is Benign according to our data. Variant chr14-70988600-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 787719.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High Homozygotes in GnomAdExome4 at 16 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PCNX1NM_014982.3 linkuse as main transcriptc.2345G>A p.Arg782His missense_variant 7/36 ENST00000304743.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PCNX1ENST00000304743.7 linkuse as main transcriptc.2345G>A p.Arg782His missense_variant 7/361 NM_014982.3 P4Q96RV3-1
PCNX1ENST00000439984.7 linkuse as main transcriptc.2311+9952G>A intron_variant 1 A1Q96RV3-4
PCNX1ENST00000554879.5 linkuse as main transcriptn.2791G>A non_coding_transcript_exon_variant 7/101
PCNX1ENST00000556846.1 linkuse as main transcriptn.271+9952G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.00234
AC:
356
AN:
152108
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000725
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00131
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00207
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00412
Gnomad OTH
AF:
0.000480
GnomAD3 exomes
AF:
0.00208
AC:
522
AN:
251316
Hom.:
1
AF XY:
0.00207
AC XY:
281
AN XY:
135850
show subpopulations
Gnomad AFR exome
AF:
0.000800
Gnomad AMR exome
AF:
0.000694
Gnomad ASJ exome
AF:
0.000695
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000294
Gnomad FIN exome
AF:
0.00120
Gnomad NFE exome
AF:
0.00382
Gnomad OTH exome
AF:
0.00147
GnomAD4 exome
AF:
0.00384
AC:
5608
AN:
1461824
Hom.:
16
Cov.:
31
AF XY:
0.00372
AC XY:
2708
AN XY:
727212
show subpopulations
Gnomad4 AFR exome
AF:
0.000866
Gnomad4 AMR exome
AF:
0.000872
Gnomad4 ASJ exome
AF:
0.000842
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000267
Gnomad4 FIN exome
AF:
0.00112
Gnomad4 NFE exome
AF:
0.00468
Gnomad4 OTH exome
AF:
0.00376
GnomAD4 genome
AF:
0.00234
AC:
356
AN:
152226
Hom.:
0
Cov.:
32
AF XY:
0.00210
AC XY:
156
AN XY:
74428
show subpopulations
Gnomad4 AFR
AF:
0.000722
Gnomad4 AMR
AF:
0.00131
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.00207
Gnomad4 NFE
AF:
0.00412
Gnomad4 OTH
AF:
0.000475
Alfa
AF:
0.00327
Hom.:
1
Bravo
AF:
0.00220
TwinsUK
AF:
0.00566
AC:
21
ALSPAC
AF:
0.00311
AC:
12
ESP6500AA
AF:
0.000908
AC:
4
ESP6500EA
AF:
0.00453
AC:
39
ExAC
AF:
0.00202
AC:
245
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.00431
EpiControl
AF:
0.00403

ClinVar

Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Likely benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpMay 18, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.076
BayesDel_addAF
Benign
-0.32
T
BayesDel_noAF
Benign
-0.23
CADD
Pathogenic
29
DANN
Uncertain
1.0
DEOGEN2
Benign
0.036
T
Eigen
Pathogenic
0.69
Eigen_PC
Pathogenic
0.68
FATHMM_MKL
Uncertain
0.90
D
LIST_S2
Uncertain
0.93
D
MetaRNN
Benign
0.0095
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.9
L
MutationTaster
Benign
1.0
D;D;D
PrimateAI
Uncertain
0.59
T
PROVEAN
Benign
-1.0
N
REVEL
Benign
0.17
Sift
Uncertain
0.0090
D
Sift4G
Benign
0.11
T
Polyphen
1.0
D
Vest4
0.28
MVP
0.082
MPC
0.13
ClinPred
0.018
T
GERP RS
5.0
Varity_R
0.19
gMVP
0.36

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.

Other links and lift over

dbSNP: rs34655198; hg19: chr14-71455317; COSMIC: COSV104985067; API