rs9317778

Variant names:

• chr13-18953052-C-G
• rs9317778

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

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 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444553.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF2P2	ENST00000444553.6	TSL:6	n.2303-159G>C		intron	N/A

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

African (AFR) AF: 0.778 AC: 32270 AN: 41472

American (AMR) AF: 0.928 AC: 14189 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.977 AC: 3389 AN: 3468

East Asian (EAS) AF: 0.960 AC: 4921 AN: 5124

South Asian (SAS) AF: 0.956 AC: 4613 AN: 4824

European-Finnish (FIN) AF: 0.958 AC: 10154 AN: 10602

Middle Eastern (MID) AF: 0.894 AC: 261 AN: 292

European-Non Finnish (NFE) AF: 0.937 AC: 63694 AN: 67980

Other (OTH) AF: 0.898 AC: 1892 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.19
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs9317778; hg19: chr13-19527192;