rs11848070

Variant names:

• chr14-71040884-G-A
• rs11848070
• NM_014982.3:c.3868-4249G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-71040884-G-A
• chr14-71040884-G-C
• chr14-71040884-G-T

Variant summary

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

The NM_014982.3(PCNX1):​c.3868-4249G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 151,830 control chromosomes in the GnomAD database, including 52,830 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 0.83 (52830 hom., cov: 29)
• Consequence: PCNX1 NM_014982.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.895
• Publications: 8 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCNX1	NM_014982.3	c.3868-4249G>A		intron_variant	Intron 19 of 35	ENST00000304743.7	NP_055797.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCNX1	ENST00000304743.7	c.3868-4249G>A		intron_variant	Intron 19 of 35	1	NM_014982.3	ENSP00000304192.2
PCNX1	ENST00000439984.7	c.3535-4249G>A		intron_variant	Intron 17 of 33	1		ENSP00000396617.3
PCNX1	ENST00000554691.5	c.1042-4249G>A		intron_variant	Intron 9 of 24	1		ENSP00000451016.1

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125675 AN: 151712 Hom.: 52770 Cov.: 29

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.939

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.829 AC: 125793 AN: 151830 Hom.: 52830 Cov.: 29 AF XY: 0.829 AC XY: 61480 AN XY: 74148

African (AFR) AF: 0.956 AC: 39629 AN: 41444

American (AMR) AF: 0.858 AC: 13071 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.827 AC: 2868 AN: 3470

East Asian (EAS) AF: 0.964 AC: 4958 AN: 5144

South Asian (SAS) AF: 0.897 AC: 4315 AN: 4812

European-Finnish (FIN) AF: 0.717 AC: 7502 AN: 10470

Middle Eastern (MID) AF: 0.938 AC: 274 AN: 292

European-Non Finnish (NFE) AF: 0.747 AC: 50725 AN: 67940

Other (OTH) AF: 0.841 AC: 1774 AN: 2110

Alfa AF: 0.799 Hom.: 101259

Bravo AF: 0.844

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.41
DANN	Benign	0.72
PhyloP100		-0.90
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: rs11848070; hg19: chr14-71507601;