rs9317778

Positions:

• chr13-18953052-C-G
• chr13-18953052-C-T

Variant summary

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

The ENST00000444553.5(PHF2P2):​n.2216-159G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.896 in 152,064 control chromosomes in the GnomAD database, including 61,492 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 0.90 (61492 hom., cov: 33)
• Consequence: PHF2P2 ENST00000444553.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHF2P2	ENST00000444553.5	n.2216-159G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136168 AN: 151944 Hom.: 61449 Cov.: 33

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.977

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.977

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.957

Gnomad FIN AF: 0.958

Gnomad MID AF: 0.895

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.897

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.896 AC: 136272 AN: 152064 Hom.: 61492 Cov.: 33 AF XY: 0.900 AC XY: 66862 AN XY: 74332

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.928

Gnomad4 ASJ AF: 0.977

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.956

Gnomad4 FIN AF: 0.958

Gnomad4 NFE AF: 0.937

Gnomad4 OTH AF: 0.898

Alfa AF: 0.907 Hom.: 3034

Bravo AF: 0.887

Asia WGS AF: 0.940 AC: 3270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9317778; hg19: chr13-19527192;