1-233312862-A-G

Position:

• chr1-233312862-A-G

Variant summary

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

The XM_047430870.1(PCNX2):​c.-97+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: PCNX2 XM_047430870.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.856

Genes affected

PCNX2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCNX2	XM_047430870.1	c.-97+14367T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.493

Alfa AF: 0.473 Hom.: 22280

Bravo AF: 0.494

Asia WGS AF: 0.472 AC: 1635 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1294330; hg19: chr1-233448608;