chr13-18960017-C-T

Position:

• chr13-18960017-C-T

Variant summary

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

The variant allele was found at a frequency of 0.302 in 186,646 control chromosomes in the GnomAD database, including 9,532 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 0.30 (7736 hom., cov: 33)
  • Exomes 𝑓: 0.29 (1796 hom.)
• Consequence: PHF2P2 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860

Genes affected

PHF2P2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHF2P2		n.18960017C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHF2P2	ENST00000444553.5	n.1507+79G>A		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46232 AN: 151952 Hom.: 7721 Cov.: 33

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.286

GnomAD4 exome AF: 0.291 AC: 10055 AN: 34576 Hom.: 1796 AF XY: 0.292 AC XY: 5269 AN XY: 18074

Gnomad4 AFR exome AF: 0.259

Gnomad4 AMR exome AF: 0.517

Gnomad4 ASJ exome AF: 0.169

Gnomad4 EAS exome AF: 0.622

Gnomad4 SAS exome AF: 0.256

Gnomad4 FIN exome AF: 0.252

Gnomad4 NFE exome AF: 0.248

Gnomad4 OTH exome AF: 0.282

GnomAD4 genome AF: 0.304 AC: 46280 AN: 152070 Hom.: 7736 Cov.: 33 AF XY: 0.311 AC XY: 23103 AN XY: 74312

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.288

Alfa AF: 0.270 Hom.: 957

Bravo AF: 0.320

Asia WGS AF: 0.423 AC: 1469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.22
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1867248; hg19: chr13-19534157;