rs425565

chr14-60137165-G-C

Variant summary

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

The NM_001330177.2(PCNX4):c.*2944G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,096 control chromosomes in the GnomAD database, including 6,897 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 (6897 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PCNX4 NM_001330177.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260

Genes affected

PCNX4 (HGNC:20349): (pecanex 4) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCNX4	NM_001330177.2	c.*2944G>C		3_prime_UTR_variant	11/11	ENST00000406854.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCNX4	ENST00000406854.6	c.*2944G>C		3_prime_UTR_variant	11/11	5	NM_001330177.2	P2
PCNX4	ENST00000317623.8	c.*2944G>C		3_prime_UTR_variant	10/10	5		A2
PCNX4	ENST00000406949.5	c.2565+11342G>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38121 AN: 151976 Hom.: 6865 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.0925

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.243

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.251 AC: 38205 AN: 152096 Hom.: 6897 Cov.: 32 AF XY: 0.252 AC XY: 18723 AN XY: 74366

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.242

Alfa AF: 0.194 Hom.: 544

Bravo AF: 0.262

Asia WGS AF: 0.353 AC: 1223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
Cadd	Benign	5.3
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs425565; hg19: chr14-60603883;