rs1867248

Variant names:

• chr13-18960017-C-A
• rs1867248

Your query was ambiguous. Multiple possible variants found:

• chr13-18960017-C-A
• chr13-18960017-C-G
• chr13-18960017-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PHF2P2 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF2P2		n.18960017C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF2P2	ENST00000444553.6	n.1594+79G>T		intron_variant	Intron 12 of 19	6

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 34694 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 18124

African (AFR) AF: 0.00 AC: 0 AN: 1800

American (AMR) AF: 0.00 AC: 0 AN: 2644

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 962

East Asian (EAS) AF: 0.00 AC: 0 AN: 1956

South Asian (SAS) AF: 0.00 AC: 0 AN: 3286

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1062

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 120

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 20870

Other (OTH) AF: 0.00 AC: 0 AN: 1994

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.63
PhyloP100		0.086

Splicing

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

Other links and lift over

dbSNP: rs1867248; hg19: chr13-19534157;