15-24777841-C-T

Variant names:

• chr15-24777841-C-T
• rs8030136
• ENST00000650707.1:n.408-29983C>T

Variant summary

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

The ENST00000650707.1(ENSG00000286110):​n.408-29983C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,156 control chromosomes in the GnomAD database, including 1,387 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 0.13 (1387 hom., cov: 32)
• Consequence: ENSG00000286110 ENST00000650707.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• 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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286110	ENST00000650707.1	n.408-29983C>T		intron_variant	Intron 3 of 6
ENSG00000286110	ENST00000651136.1	n.1531-29983C>T		intron_variant	Intron 9 of 14
PWRN1	ENST00000652025.1	n.1488-29983C>T		intron_variant	Intron 10 of 13

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19049 AN: 152038 Hom.: 1384 Cov.: 32

Gnomad AFR AF: 0.0601

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.0595

Gnomad SAS AF: 0.0881

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.125 AC: 19049 AN: 152156 Hom.: 1387 Cov.: 32 AF XY: 0.123 AC XY: 9114 AN XY: 74378

African (AFR) AF: 0.0600 AC: 2493 AN: 41536

American (AMR) AF: 0.150 AC: 2298 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 809 AN: 3470

East Asian (EAS) AF: 0.0595 AC: 308 AN: 5180

South Asian (SAS) AF: 0.0882 AC: 425 AN: 4820

European-Finnish (FIN) AF: 0.112 AC: 1188 AN: 10576

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11089 AN: 67978

Other (OTH) AF: 0.133 AC: 281 AN: 2110

Alfa AF: 0.139 Hom.: 219

Bravo AF: 0.129

Asia WGS AF: 0.0670 AC: 234 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.4
DANN	Benign	0.69
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs8030136; hg19: chr15-25022988;