rs1889574

Variant names:

• chr13-18955504-G-A
• rs1889574

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 0.409 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
• Publications: 4 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=-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 rank	MANE	Protein	UniProt
PHF2P2		n.18955504G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF2P2	ENST00000444553.6	n.2186+33C>T		intron_variant	Intron 15 of 19	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

African (AFR) AF: 0.550 AC: 14360 AN: 26092

American (AMR) AF: 0.634 AC: 24716 AN: 38964

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 6153 AN: 22894

East Asian (EAS) AF: 0.621 AC: 22294 AN: 35880

South Asian (SAS) AF: 0.295 AC: 22532 AN: 76268

European-Finnish (FIN) AF: 0.384 AC: 18927 AN: 49298

Middle Eastern (MID) AF: 0.262 AC: 1336 AN: 5100

European-Non Finnish (NFE) AF: 0.394 AC: 315360 AN: 801004

Other (OTH) AF: 0.406 AC: 19371 AN: 47756

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

African (AFR) AF: 0.552 AC: 22852 AN: 41432

American (AMR) AF: 0.537 AC: 8210 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 975 AN: 3470

East Asian (EAS) AF: 0.618 AC: 3179 AN: 5142

South Asian (SAS) AF: 0.300 AC: 1444 AN: 4814

European-Finnish (FIN) AF: 0.385 AC: 4058 AN: 10550

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25879 AN: 67928

Other (OTH) AF: 0.407 AC: 859 AN: 2110

Alfa AF: 0.390 Hom.: 22081

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
PhyloP100		-0.24
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

Other links and lift over

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