rs9553323

Variant names:

• chr13-19051200-G-A
• rs9553323
• ENST00000444553.6:n.560C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-19051200-G-A
• chr13-19051200-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000444553.6(PHF2P2):​n.560C>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 0.461 in 896,846 control chromosomes in the GnomAD database, including 106,239 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 0.42 (15996 hom., cov: 34)
  • Exomes 𝑓: 0.47 (90243 hom.)
• Consequence: PHF2P2 ENST00000444553.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990
• Publications: 4 publications found

Genes affected

PHF2P2 (HGNC:38808): (PHD finger protein 2 pseudogene 2)

PHF2P1 (HGNC:30241): (PHD finger protein 2 pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF2P1		n.19051200G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF2P2	ENST00000444553.6	n.560C>T		non_coding_transcript_exon_variant	Exon 4 of 20	6

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64561 AN: 152016 Hom.: 15979 Cov.: 34

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.436

GnomAD4 exome AF: 0.469 AC: 349082 AN: 744712 Hom.: 90243 Cov.: 11 AF XY: 0.474 AC XY: 187885 AN XY: 396752

African (AFR) AF: 0.128 AC: 2889 AN: 22528

American (AMR) AF: 0.679 AC: 28982 AN: 42668

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 8340 AN: 21254

East Asian (EAS) AF: 0.756 AC: 26566 AN: 35140

South Asian (SAS) AF: 0.504 AC: 36527 AN: 72456

European-Finnish (FIN) AF: 0.465 AC: 23012 AN: 49528

Middle Eastern (MID) AF: 0.293 AC: 1228 AN: 4192

European-Non Finnish (NFE) AF: 0.446 AC: 205393 AN: 460930

Other (OTH) AF: 0.448 AC: 16145 AN: 36016

GnomAD4 genome AF: 0.425 AC: 64582 AN: 152134 Hom.: 15996 Cov.: 34 AF XY: 0.428 AC XY: 31807 AN XY: 74338

African (AFR) AF: 0.162 AC: 6730 AN: 41542

American (AMR) AF: 0.580 AC: 8869 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1366 AN: 3468

East Asian (EAS) AF: 0.720 AC: 3702 AN: 5140

South Asian (SAS) AF: 0.516 AC: 2485 AN: 4812

European-Finnish (FIN) AF: 0.457 AC: 4844 AN: 10594

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.515 AC: 35040 AN: 67974

Other (OTH) AF: 0.440 AC: 929 AN: 2110

Alfa AF: 0.475 Hom.: 4201

Bravo AF: 0.424

Asia WGS AF: 0.577 AC: 2004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	7.6
DANN	Benign	0.52
PhyloP100		0.099

Splicing

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

Other links and lift over

dbSNP: rs9553323; hg19: chr13-19625340;