rs35600665

chr15-24496144-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000565295.6(PWRN1):n.667+4517C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 151,910 control chromosomes in the GnomAD database, including 3,934 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 0.20 (3934 hom., cov: 33)
• Consequence: PWRN1 ENST00000565295.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

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]

LOC105370733 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370733	XR_007064536.1	n.1036+4517C>T		intron_variant, non_coding_transcript_variant
LOC105370733	XR_007064537.1	n.795-12717C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PWRN1	ENST00000565295.6	n.667+4517C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31092 AN: 151792 Hom.: 3932 Cov.: 33

Gnomad AFR AF: 0.0919

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.205 AC: 31092 AN: 151910 Hom.: 3934 Cov.: 33 AF XY: 0.204 AC XY: 15153 AN XY: 74252

Gnomad4 AFR AF: 0.0919

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.203

Alfa AF: 0.234 Hom.: 1396

Bravo AF: 0.193

Asia WGS AF: 0.183 AC: 634 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.38
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35600665; hg19: chr15-24741291;