rs16858621

chr1-233079114-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014801.4(PCNX2):c.4076+10947G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0953 in 152,158 control chromosomes in the GnomAD database, including 752 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.095 (752 hom., cov: 31)
• Consequence: PCNX2 NM_014801.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCNX2	NM_014801.4	c.4076+10947G>T		intron_variant		ENST00000258229.14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCNX2	ENST00000258229.14	c.4076+10947G>T		intron_variant		5	NM_014801.4	A2
PCNX2	ENST00000475463.6	c.*1328-13453G>T		intron_variant, NMD_transcript_variant		1
PCNX2	ENST00000462233.5	c.1140+10947G>T		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0953 AC: 14492 AN: 152040 Hom.: 752 Cov.: 31

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0682

Gnomad ASJ AF: 0.0749

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.0657

Gnomad FIN AF: 0.0975

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0936

Gnomad OTH AF: 0.105

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0953 AC: 14503 AN: 152158 Hom.: 752 Cov.: 31 AF XY: 0.0945 AC XY: 7031 AN XY: 74382

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.0681

Gnomad4 ASJ AF: 0.0749

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.0657

Gnomad4 FIN AF: 0.0975

Gnomad4 NFE AF: 0.0936

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0958 Hom.: 621

Bravo AF: 0.0939

Asia WGS AF: 0.100 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.9
Dann	Benign	0.55

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

Other links and lift over

dbSNP: rs16858621; hg19: chr1-233214860;