chr15-24719450-G-A

Variant names:

• chr15-24719450-G-A
• rs8027714
• ENST00000650707.1:n.408-88374G>A

Variant summary

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

The ENST00000650707.1(ENSG00000286110):​n.408-88374G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,104 control chromosomes in the GnomAD database, including 1,808 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 0.10 (1808 hom., cov: 32)
• Consequence: ENSG00000286110 ENST00000650707.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995
• Publications: 13 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 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.408-88374G>A		intron_variant	Intron 3 of 6
ENSG00000286110	ENST00000651136.1	n.1531-88374G>A		intron_variant	Intron 9 of 14
PWRN1	ENST00000652025.1	n.1488-88374G>A		intron_variant	Intron 10 of 13

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15534 AN: 151986 Hom.: 1801 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.0469

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.0292

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0350

Gnomad OTH AF: 0.0827

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

GnomAD4 genome AF: 0.102 AC: 15567 AN: 152104 Hom.: 1808 Cov.: 32 AF XY: 0.0988 AC XY: 7348 AN XY: 74360

African (AFR) AF: 0.284 AC: 11773 AN: 41436

American (AMR) AF: 0.0468 AC: 715 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00490 AC: 17 AN: 3468

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5166

South Asian (SAS) AF: 0.0307 AC: 148 AN: 4822

European-Finnish (FIN) AF: 0.0292 AC: 309 AN: 10594

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0350 AC: 2382 AN: 68010

Other (OTH) AF: 0.0823 AC: 174 AN: 2114

Alfa AF: 0.613 Hom.: 13233

Bravo AF: 0.112

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.16
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs8027714; hg19: chr15-24964597;