15-23948435-G-T

Position:

• chr15-23948435-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PWRN4	ENST00000652183.1	n.440+6606G>T		intron_variant

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

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.821

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.692

Alfa AF: 0.765 Hom.: 64094

Bravo AF: 0.673

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4778359; hg19: chr15-24193582;