rs1294330

Variant names:

• chr1-233312862-A-G
• rs1294330
• XM_047430870.1:c.-97+14367T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-233312862-A-G
• chr1-233312862-A-T

Variant summary

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

The ENST00000771586.1(ENSG00000300424):​n.92+14367T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 151,610 control chromosomes in the GnomAD database, including 19,104 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 0.50 (19104 hom., cov: 30)
• Consequence: ENSG00000300424 ENST00000771586.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.856
• Publications: 3 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]

ENSG00000300424 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000771586.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300424	ENST00000771586.1		n.92+14367T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75445 AN: 151492 Hom.: 19083 Cov.: 30

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.498 AC: 75520 AN: 151610 Hom.: 19104 Cov.: 30 AF XY: 0.501 AC XY: 37119 AN XY: 74108

African (AFR) AF: 0.550 AC: 22708 AN: 41324

American (AMR) AF: 0.493 AC: 7497 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1430 AN: 3470

East Asian (EAS) AF: 0.370 AC: 1907 AN: 5156

South Asian (SAS) AF: 0.562 AC: 2705 AN: 4810

European-Finnish (FIN) AF: 0.560 AC: 5854 AN: 10456

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.468 AC: 31787 AN: 67872

Other (OTH) AF: 0.493 AC: 1036 AN: 2102

Alfa AF: 0.474 Hom.: 28473

Bravo AF: 0.494

Asia WGS AF: 0.472 AC: 1635 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.34
PhyloP100		-0.86

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1294330;

hg19: chr1-233448608;