rs2810114

Positions:

• chr14-70928887-C-A

Variant summary

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

The NM_014982.3(PCNX1):​c.154-18028C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 152,030 control chromosomes in the GnomAD database, including 37,508 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 0.70 (37508 hom., cov: 31)
• Consequence: PCNX1 NM_014982.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

PCNX1 (HGNC:19740): (pecanex 1) This gene encodes an evolutionarily conserved transmembrane protein similar to the pecanex protein in Drosophila. The fly protein is a component of the Notch signaling pathway, which functions in several developmental processes. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCNX1	NM_014982.3	c.154-18028C>A		intron_variant		ENST00000304743.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCNX1	ENST00000304743.7	c.154-18028C>A		intron_variant		1	NM_014982.3	P4
PCNX1	ENST00000439984.7	c.154-18028C>A		intron_variant		1		A1
PCNX1	ENST00000554879.5	n.600-18028C>A		intron_variant, non_coding_transcript_variant		1
PCNX1	ENST00000554292.1	n.335-13986C>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106716 AN: 151914 Hom.: 37460 Cov.: 31

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.703 AC: 106828 AN: 152030 Hom.: 37508 Cov.: 31 AF XY: 0.703 AC XY: 52209 AN XY: 74304

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.738

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.713

Alfa AF: 0.713 Hom.: 50814

Bravo AF: 0.692

Asia WGS AF: 0.762 AC: 2643 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.19
DANN	Benign	0.29

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: rs2810114; hg19: chr14-71395604;