20-12380707-C-T

Variant names:

• chr20-12380707-C-T
• rs6033392
• ENST00000414718.1:n.652C>T

Variant summary

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

The ENST00000414718.1(PA2G4P2):​n.652C>T 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 0.0182 in 1,384,834 control chromosomes in the GnomAD database, including 429 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 0.033 (141 hom., cov: 32)
  • Exomes 𝑓: 0.016 (288 hom.)
• Consequence: PA2G4P2 ENST00000414718.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.59

Genes affected

PA2G4P2 (HGNC:16531): (proliferation-associated 2G4 pseudogene 2)

LOC124904870 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PA2G4P2		n.12380707C>T		intragenic_variant
LOC124904870	XR_007067531.1	n.165-6441G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PA2G4P2	ENST00000414718.1	n.652C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.0327 AC: 4977 AN: 152094 Hom.: 141 Cov.: 32

Gnomad AFR AF: 0.0717

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0204

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0261

Gnomad FIN AF: 0.0169

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0187

Gnomad OTH AF: 0.0215

GnomAD4 exome AF: 0.0164 AC: 20171 AN: 1232622 Hom.: 288 Cov.: 21 AF XY: 0.0166 AC XY: 10341 AN XY: 624748

Gnomad4 AFR exome AF: 0.0679

Gnomad4 AMR exome AF: 0.0132

Gnomad4 ASJ exome AF: 0.0130

Gnomad4 EAS exome AF: 0.000208

Gnomad4 SAS exome AF: 0.0224

Gnomad4 FIN exome AF: 0.0150

Gnomad4 NFE exome AF: 0.0151

Gnomad4 OTH exome AF: 0.0180

GnomAD4 genome AF: 0.0328 AC: 4986 AN: 152212 Hom.: 141 Cov.: 32 AF XY: 0.0325 AC XY: 2420 AN XY: 74428

Gnomad4 AFR AF: 0.0717

Gnomad4 AMR AF: 0.0203

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.000388

Gnomad4 SAS AF: 0.0261

Gnomad4 FIN AF: 0.0169

Gnomad4 NFE AF: 0.0187

Gnomad4 OTH AF: 0.0213

Alfa AF: 0.0263 Hom.: 7

Bravo AF: 0.0347

Asia WGS AF: 0.0210 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	11
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6033392; hg19: chr20-12361355;