1-233017164-A-AAAAGCAAGATTTTGAGTCCTCACAGCTATTCG

Variant names:

• chr1-233017164-A-AAAAGCAAGATTTTGAGTCCTCACAGCTATTCG
• NM_014801.4:c.4606-11_4606-10insCGAATAGCTGTGAGGACTCAAAATCTTGCTTT

Variant summary

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

The NM_014801.4(PCNX2):​c.4606-11_4606-10insCGAATAGCTGTGAGGACTCAAAATCTTGCTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000715 in 1,398,150 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: not found (cov: 22)
  • Exomes 𝑓: 7.2e-7 (0 hom.)
• Consequence: PCNX2 NM_014801.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

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]

ACMG classification

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	c.4606-11_4606-10insCGAATAGCTGTGAGGACTCAAAATCTTGCTTT		intron_variant	Intron 26 of 33	ENST00000258229.14	NP_055616.3

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome AF: 7.15e-7 AC: 1 AN: 1398150 Hom.: 0 Cov.: 32 AF XY: 0.00000145 AC XY: 1 AN XY: 689624

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.44e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-233152910;