15-24772048-T-C

Variant names:

• chr15-24772048-T-C
• rs975963
• ENST00000650707.1:n.408-35776T>C

Variant summary

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

The ENST00000650707.1(ENSG00000286110):​n.408-35776T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,094 control chromosomes in the GnomAD database, including 32,907 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 0.65 (32907 hom., cov: 33)
• Consequence: ENSG00000286110 ENST00000650707.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.610
• Publications: 3 publications found

Genes affected

ENSG00000286110 (HGNC:):

PWRN1 (HGNC:33235): (Prader-Willi region non-protein coding RNA 1) This gene is located in the Prader-Willi syndrome (PWS) region of chromosome 15, which is known to undergo imprinting. The transcript is believed to be non-coding. It is bi-allelically expressed in testis and kidney, but mono-allelically expressed from the paternal allele in brain. This gene is poly-adenylated and is known to undergo alternative splicing. Transcript variants may represent part of a complex imprinting center-SNURF-SNRPN transcription unit. The contribution of this gene to the PWS phenotype is unknown, but it has been suggested that it may play a role in establishing paternal imprinting in the PWS region, perhaps by maintaining the paternal allele in an open chromatin configuration. [provided by RefSeq, Sep 2009]

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 (AFR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650707.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286110	ENST00000650707.1		n.408-35776T>C		intron	N/A
	ENSG00000286110	ENST00000651136.1		n.1531-35776T>C		intron	N/A
	PWRN1	ENST00000652025.1		n.1488-35776T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98825 AN: 151976 Hom.: 32865 Cov.: 33

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.650 AC: 98923 AN: 152094 Hom.: 32907 Cov.: 33 AF XY: 0.650 AC XY: 48291 AN XY: 74308

African (AFR) AF: 0.796 AC: 33050 AN: 41514

American (AMR) AF: 0.600 AC: 9176 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2318 AN: 3468

East Asian (EAS) AF: 0.686 AC: 3540 AN: 5162

South Asian (SAS) AF: 0.633 AC: 3050 AN: 4820

European-Finnish (FIN) AF: 0.574 AC: 6051 AN: 10550

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39644 AN: 67970

Other (OTH) AF: 0.651 AC: 1372 AN: 2106

Alfa AF: 0.610 Hom.: 3558

Bravo AF: 0.661

Asia WGS AF: 0.700 AC: 2430 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.48
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs975963; hg19: chr15-25017195;