ENST00000652183.1:n.784+24783T>C

Variant names:

• chr15-24003994-T-C
• rs11630255
• ENST00000652183.1:n.784+24783T>C

Variant summary

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

The ENST00000652183.1(PWRN4):​n.784+24783T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 151,768 control chromosomes in the GnomAD database, including 8,186 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 0.32 (8186 hom., cov: 32)
• Consequence: PWRN4 ENST00000652183.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.86
• Publications: 2 publications found

Genes affected

PWRN4 (HGNC:49130): (Prader-Willi region non-protein coding RNA 4)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652183.1. 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
	PWRN4	NR_126392.1		n.445+559T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PWRN4	ENST00000652183.1		n.784+24783T>C		intron	N/A
	PWRN4	ENST00000661343.1		n.487+24783T>C		intron	N/A
	PWRN4	ENST00000663707.1		n.435+24783T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49262 AN: 151652 Hom.: 8168 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.325 AC: 49306 AN: 151768 Hom.: 8186 Cov.: 32 AF XY: 0.318 AC XY: 23577 AN XY: 74146

African (AFR) AF: 0.339 AC: 14038 AN: 41402

American (AMR) AF: 0.270 AC: 4104 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 980 AN: 3470

East Asian (EAS) AF: 0.169 AC: 870 AN: 5134

South Asian (SAS) AF: 0.284 AC: 1366 AN: 4806

European-Finnish (FIN) AF: 0.270 AC: 2840 AN: 10516

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.356 AC: 24185 AN: 67902

Other (OTH) AF: 0.301 AC: 635 AN: 2110

Alfa AF: 0.342 Hom.: 4725

Bravo AF: 0.324

Asia WGS AF: 0.237 AC: 824 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	0.47
DANN	Benign	0.38
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs11630255; hg19: chr15-24249141;