rs12801636

Variant names:

• chr11-65623846-G-A
• rs12801636
• NM_032223.4:c.2512-83G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-65623846-G-A
• chr11-65623846-G-C

Variant summary

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

The NM_032223.4(PCNX3):​c.2512-83G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 1,591,746 control chromosomes in the GnomAD database, including 49,883 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 0.25 (5247 hom., cov: 33)
  • Exomes 𝑓: 0.24 (44636 hom.)
• Consequence: PCNX3 NM_032223.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428
• Publications: 106 publications found

Genes affected

PCNX3 (HGNC:18760): (pecanex 3) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032223.4. 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
	PCNX3	NM_032223.4	MANE Select	c.2512-83G>A		intron	N/A	NP_115599.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCNX3	ENST00000355703.4	TSL:5 MANE Select	c.2512-83G>A		intron	N/A	ENSP00000347931.3	Q9H6A9-1
	PCNX3	ENST00000913358.1		c.2551-83G>A		intron	N/A	ENSP00000583417.1
	PCNX3	ENST00000913354.1		c.2548-83G>A		intron	N/A	ENSP00000583413.1

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38667 AN: 152062 Hom.: 5232 Cov.: 33

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.237

GnomAD4 exome AF: 0.241 AC: 346701 AN: 1439564 Hom.: 44636 Cov.: 30 AF XY: 0.240 AC XY: 171825 AN XY: 717338

African (AFR) AF: 0.257 AC: 8496 AN: 33032

American (AMR) AF: 0.473 AC: 20926 AN: 44272

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 5249 AN: 25922

East Asian (EAS) AF: 0.472 AC: 18664 AN: 39512

South Asian (SAS) AF: 0.248 AC: 21263 AN: 85734

European-Finnish (FIN) AF: 0.205 AC: 10174 AN: 49746

Middle Eastern (MID) AF: 0.234 AC: 1341 AN: 5720

European-Non Finnish (NFE) AF: 0.224 AC: 245516 AN: 1095940

Other (OTH) AF: 0.253 AC: 15072 AN: 59686

GnomAD4 genome AF: 0.254 AC: 38717 AN: 152182 Hom.: 5247 Cov.: 33 AF XY: 0.260 AC XY: 19313 AN XY: 74406

African (AFR) AF: 0.259 AC: 10751 AN: 41528

American (AMR) AF: 0.389 AC: 5945 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 737 AN: 3468

East Asian (EAS) AF: 0.415 AC: 2146 AN: 5168

South Asian (SAS) AF: 0.261 AC: 1260 AN: 4830

European-Finnish (FIN) AF: 0.196 AC: 2079 AN: 10604

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15050 AN: 67972

Other (OTH) AF: 0.238 AC: 503 AN: 2110

Alfa AF: 0.241 Hom.: 20550

Bravo AF: 0.271

Asia WGS AF: 0.368 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	6.8
DANN	Benign	0.83
PhyloP100		0.43
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		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: rs12801636; hg19: chr11-65391317; COSMIC: COSV63135577; COSMIC: COSV63135577;