rs1889574

Positions:

• chr13-18955504-G-A

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 0.409 in 1,255,188 control chromosomes in the GnomAD database, including 109,471 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 0.45 (15957 hom., cov: 32)
  • Exomes 𝑓: 0.40 (93514 hom.)
• Consequence: PHF2P2 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.242

Genes affected

PHF2P2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHF2P2		n.18955504G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHF2P2	ENST00000444553.5	n.2099+33C>T		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67762 AN: 151814 Hom.: 15937 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.406

GnomAD4 exome AF: 0.403 AC: 445049 AN: 1103256 Hom.: 93514 Cov.: 14 AF XY: 0.397 AC XY: 222543 AN XY: 561234

Gnomad4 AFR exome AF: 0.550

Gnomad4 AMR exome AF: 0.634

Gnomad4 ASJ exome AF: 0.269

Gnomad4 EAS exome AF: 0.621

Gnomad4 SAS exome AF: 0.295

Gnomad4 FIN exome AF: 0.384

Gnomad4 NFE exome AF: 0.394

Gnomad4 OTH exome AF: 0.406

GnomAD4 genome AF: 0.447 AC: 67838 AN: 151932 Hom.: 15957 Cov.: 32 AF XY: 0.446 AC XY: 33124 AN XY: 74244

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.537

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.407

Alfa AF: 0.382 Hom.: 17021

Bravo AF: 0.467

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.49
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1889574; hg19: chr13-19529644; COSMIC: COSV69406126;