14-70988600-G-A
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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
NM_014982.3 missense
Scores
2
5
11
Clinical Significance
Conservation
PhyloP100: 6.23
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]
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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 |
---|---|---|---|---|---|---|---|
PCNX1 | NM_014982.3 | c.2345G>A | p.Arg782His | missense_variant | 7/36 | ENST00000304743.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCNX1 | ENST00000304743.7 | c.2345G>A | p.Arg782His | missense_variant | 7/36 | 1 | NM_014982.3 | P4 | |
PCNX1 | ENST00000439984.7 | c.2311+9952G>A | intron_variant | 1 | A1 | ||||
PCNX1 | ENST00000554879.5 | n.2791G>A | non_coding_transcript_exon_variant | 7/10 | 1 | ||||
PCNX1 | ENST00000556846.1 | n.271+9952G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00234 AC: 356AN: 152108Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00208 AC: 522AN: 251316Hom.: 1 AF XY: 0.00207 AC XY: 281AN XY: 135850
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GnomAD4 exome AF: 0.00384 AC: 5608AN: 1461824Hom.: 16 Cov.: 31 AF XY: 0.00372 AC XY: 2708AN XY: 727212
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GnomAD4 genome AF: 0.00234 AC: 356AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.00210 AC XY: 156AN XY: 74428
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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 submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 18, 2018 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Benign
T
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at