rs16858621

Variant names:

• chr1-233079114-C-A
• rs16858621
• NM_014801.4:c.4076+10947G>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.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
• Publications: 1 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
PCNX2	NM_014801.4	c.4076+10947G>T		intron_variant	Intron 23 of 33	ENST00000258229.14	NP_055616.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCNX2	ENST00000258229.14	c.4076+10947G>T		intron_variant	Intron 23 of 33	5	NM_014801.4	ENSP00000258229.8
PCNX2	ENST00000475463.6	n.*1328-13453G>T		intron_variant	Intron 16 of 16	1		ENSP00000429360.1
PCNX2	ENST00000462233.5	n.1139+10947G>T		intron_variant	Intron 10 of 19	2		ENSP00000428488.1

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

African (AFR) AF: 0.105 AC: 4369 AN: 41500

American (AMR) AF: 0.0681 AC: 1040 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0749 AC: 260 AN: 3472

East Asian (EAS) AF: 0.158 AC: 813 AN: 5158

South Asian (SAS) AF: 0.0657 AC: 317 AN: 4824

European-Finnish (FIN) AF: 0.0975 AC: 1033 AN: 10592

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0936 AC: 6367 AN: 68014

Other (OTH) AF: 0.103 AC: 218 AN: 2112

Alfa AF: 0.0948 Hom.: 799

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
PhyloP100		0.21
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: rs16858621; hg19: chr1-233214860;