15-23948435-G-T

Variant names:

• chr15-23948435-G-T
• rs4778359
• ENST00000652183.1:n.440+6606G>T

Variant summary

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

The ENST00000652183.1(PWRN4):​n.440+6606G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 152,062 control chromosomes in the GnomAD database, including 36,391 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 0.67 (36391 hom., cov: 33)
• Consequence: PWRN4 ENST00000652183.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 6 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PWRN4	ENST00000652183.1		n.440+6606G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102255 AN: 151942 Hom.: 36377 Cov.: 33

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.673 AC: 102307 AN: 152062 Hom.: 36391 Cov.: 33 AF XY: 0.674 AC XY: 50123 AN XY: 74312

African (AFR) AF: 0.426 AC: 17666 AN: 41470

American (AMR) AF: 0.781 AC: 11934 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2700 AN: 3470

East Asian (EAS) AF: 0.821 AC: 4234 AN: 5160

South Asian (SAS) AF: 0.760 AC: 3665 AN: 4822

European-Finnish (FIN) AF: 0.655 AC: 6907 AN: 10542

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52830 AN: 68008

Other (OTH) AF: 0.692 AC: 1456 AN: 2104

Alfa AF: 0.758 Hom.: 86952

Bravo AF: 0.673

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.14
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4778359;

hg19: chr15-24193582;