rs4649444

Variant names:

• chr1-233203465-C-A
• rs4649444
• NM_014801.4:c.2864-3201G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-233203465-C-A
• chr1-233203465-C-G
• chr1-233203465-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014801.4(PCNX2):​c.2864-3201G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,794 control chromosomes in the GnomAD database, including 7,295 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 0.29 (7295 hom., cov: 32)
• Consequence: PCNX2 NM_014801.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 4 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]

ENSG00000298828 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

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.2864-3201G>T		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.2864-3201G>T		intron	N/A	ENSP00000258229.8
	PCNX2	ENST00000475463.6	TSL:1	n.*354-3201G>T		intron	N/A	ENSP00000429360.1
	PCNX2	ENST00000912675.1		c.2691+14434G>T		intron	N/A	ENSP00000582734.1

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44492 AN: 151676 Hom.: 7280 Cov.: 32

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.294 AC: 44560 AN: 151794 Hom.: 7295 Cov.: 32 AF XY: 0.296 AC XY: 21957 AN XY: 74156

African (AFR) AF: 0.404 AC: 16712 AN: 41378

American (AMR) AF: 0.378 AC: 5774 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 918 AN: 3470

East Asian (EAS) AF: 0.562 AC: 2912 AN: 5182

South Asian (SAS) AF: 0.211 AC: 1007 AN: 4778

European-Finnish (FIN) AF: 0.234 AC: 2456 AN: 10512

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13888 AN: 67908

Other (OTH) AF: 0.310 AC: 653 AN: 2106

Alfa AF: 0.261 Hom.: 2951

Bravo AF: 0.316

Asia WGS AF: 0.386 AC: 1342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.44
DANN	Benign	0.36
PhyloP100		-0.037
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4649444; hg19: chr1-233339211;