rs1540053

Positions:

• chr4-99160997-C-T

Variant summary

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

The NR_028270.1(PCNAP1):​n.651G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 190,614 control chromosomes in the GnomAD database, including 54,857 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 0.75 (42657 hom., cov: 32)
  • Exomes 𝑓: 0.79 (12200 hom.)
• Consequence: PCNAP1 NR_028270.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05

Genes affected

PCNAP1 (HGNC:8732): (proliferating cell nuclear antigen pseudogene 1)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCNAP1	NR_028270.1	n.651G>A		non_coding_transcript_exon_variant	1/1
LOC100507053	NR_037884.1	n.3714+3418C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCNAP1	ENST00000505363.2	n.649G>A		non_coding_transcript_exon_variant	1/1
	ENST00000595299.1	n.269G>A		non_coding_transcript_exon_variant	1/1
	ENST00000500358.6	n.3714+3418C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113251 AN: 151954 Hom.: 42641 Cov.: 32

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.751

GnomAD4 exome AF: 0.794 AC: 30593 AN: 38542 Hom.: 12200 Cov.: 0 AF XY: 0.789 AC XY: 18264 AN XY: 23134

Gnomad4 AFR exome AF: 0.665

Gnomad4 AMR exome AF: 0.838

Gnomad4 ASJ exome AF: 0.741

Gnomad4 EAS exome AF: 0.999

Gnomad4 SAS exome AF: 0.864

Gnomad4 FIN exome AF: 0.713

Gnomad4 NFE exome AF: 0.768

Gnomad4 OTH exome AF: 0.781

GnomAD4 genome AF: 0.745 AC: 113310 AN: 152072 Hom.: 42657 Cov.: 32 AF XY: 0.750 AC XY: 55750 AN XY: 74352

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.888

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.753

Alfa AF: 0.765 Hom.: 81055

Bravo AF: 0.743

Asia WGS AF: 0.909 AC: 3160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	4.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1540053; hg19: chr4-100082154;