Genetic Variant PCNX2:c.4606-11_4606-10insAGAATAGCTATGAGGACTCAAAATCTTGCTTT (chr1-233017164-A-AAAAGCAAGATTTTGAGTCCTCATAGCTATTCT) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_014801.4(PCNX2):c.4606-11_4606-10insAGAATAGCTATGAGGACTCAAAATCTTGCTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000194 in 1,549,830 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 22)

Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

PCNX2
NM_014801.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.581

Variant links:

Genes affected

PCNX2 (HGNC:8736): (pecanex 2) This gene contains coding mononucleotide repeats that are associated with tumors of high mcrosatellite instability (MSI-H). Defects in this gene are involved in the tumorigenesis of MSI-H colorectal carcinomas. [provided by RefSeq, Jun 2016]

PCNX2 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCNX2	NM_014801.4 link	c.4606-11_4606-10insAGAATAGCTATGAGGACTCAAAATCTTGCTTT		intron_variant	Intron 26 of 33	ENST00000258229.14	NP_055616.3	A6NKB5-1B3KNZ5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PCNX2	ENST00000258229.14 link	c.4606-11_4606-10insAGAATAGCTATGAGGACTCAAAATCTTGCTTT	intron_variant	Intron 26 of 33	5	NM_014801.4	ENSP00000258229.8	A6NKB5-1
PCNX2	ENST00000344698.6 link	c.562-11_562-10insAGAATAGCTATGAGGACTCAAAATCTTGCTTT	intron_variant	Intron 3 of 9	2		ENSP00000340759.2	A6NKB5-3
PCNX2	ENST00000462233.5 link	n.1415-11_1415-10insAGAATAGCTATGAGGACTCAAAATCTTGCTTT	intron_variant	Intron 12 of 19	2		ENSP00000428488.1	H0YB15
PCNX2	ENST00000522067.1 link	n.488-11_488-10insAGAATAGCTATGAGGACTCAAAATCTTGCTTT	intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.00000659

AC:

AN:

151680

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000243

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00000143

AC:

AN:

1398150

Hom.:

Cov.:

AF XY:

0.00000145

AC XY:

AN XY:

689624

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000260

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.00000659

AC:

AN:

151680

Hom.:

Cov.:

AF XY:

0.0000135

AC XY:

AN XY:

74040

show subpopulations

Gnomad4 AFR

AF:

0.0000243

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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