chr13-18955504-G-A

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.

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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF2P2	ENST00000444553.6	TSL:6	n.2186+33C>T		intron	N/A

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 v4.9

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;