NM_014801.4:c.4606-11_4606-10insAGTATAGCTGTGAGGACTCAAAATCTTGCTTT

Variant names:

• chr1-233017164-A-AAAAGCAAGATTTTGAGTCCTCACAGCTATACT
• rs11271054
• NM_014801.4:c.4606-11_4606-10insAGTATAGCTGTGAGGACTCAAAATCTTGCTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_014801.4(PCNX2):​c.4606-11_4606-10insAGTATAGCTGTGAGGACTCAAAATCTTGCTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000143 in 1,398,150 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 22)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: PCNX2 NM_014801.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014801.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCNX2	NM_014801.4	MANE Select	c.4606-11_4606-10insAGTATAGCTGTGAGGACTCAAAATCTTGCTTT		intron	N/A	NP_055616.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCNX2	ENST00000258229.14	TSL:5 MANE Select	c.4606-11_4606-10insAGTATAGCTGTGAGGACTCAAAATCTTGCTTT		intron	N/A	ENSP00000258229.8	A6NKB5-1
	PCNX2	ENST00000912675.1		c.4231-11_4231-10insAGTATAGCTGTGAGGACTCAAAATCTTGCTTT		intron	N/A	ENSP00000582734.1
	PCNX2	ENST00000344698.6	TSL:2	c.562-11_562-10insAGTATAGCTGTGAGGACTCAAAATCTTGCTTT		intron	N/A	ENSP00000340759.2	A6NKB5-3

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome AF: 0.00000143 AC: 2 AN: 1398150 Hom.: 0 Cov.: 32 AF XY: 0.00000290 AC XY: 2 AN XY: 689624

African (AFR) AF: 0.00 AC: 0 AN: 31710

American (AMR) AF: 0.00 AC: 0 AN: 43364

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25466

East Asian (EAS) AF: 0.00 AC: 0 AN: 38534

South Asian (SAS) AF: 0.00 AC: 0 AN: 83636

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52950

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5132

European-Non Finnish (NFE) AF: 9.44e-7 AC: 1 AN: 1059654

Other (OTH) AF: 0.0000173 AC: 1 AN: 57704

GnomAD4 genome Cov.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs11271054; hg19: chr1-233152910;