NM_014982.3:c.154-18028C>A

Variant names:

• chr14-70928887-C-A
• rs2810114
• NM_014982.3:c.154-18028C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014982.3. 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
	PCNX1	NM_014982.3	MANE Select	c.154-18028C>A		intron	N/A	NP_055797.2	Q96RV3-1
	PCNX1	NM_001308160.2		c.154-18028C>A		intron	N/A	NP_001295089.1	Q96RV3-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCNX1	ENST00000304743.7	TSL:1 MANE Select	c.154-18028C>A		intron	N/A	ENSP00000304192.2	Q96RV3-1
	PCNX1	ENST00000439984.7	TSL:1	c.154-18028C>A		intron	N/A	ENSP00000396617.3	Q96RV3-4
	PCNX1	ENST00000554879.5	TSL:1	n.600-18028C>A		intron	N/A

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

African (AFR) AF: 0.692 AC: 28703 AN: 41480

American (AMR) AF: 0.643 AC: 9814 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2379 AN: 3470

East Asian (EAS) AF: 0.654 AC: 3380 AN: 5166

South Asian (SAS) AF: 0.763 AC: 3682 AN: 4826

European-Finnish (FIN) AF: 0.738 AC: 7781 AN: 10542

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.717 AC: 48752 AN: 67956

Other (OTH) AF: 0.713 AC: 1505 AN: 2112

Alfa AF: 0.713 Hom.: 125661

Bravo AF: 0.692

Asia WGS AF: 0.762 AC: 2643 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.19
DANN	Benign	0.29
PhyloP100		-1.4
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: rs2810114; hg19: chr14-71395604;