rs7496441

Variant names:

• chr15-24482084-A-G
• rs7496441
• ENST00000562244.2:n.403-9382A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-24482084-A-G
• chr15-24482084-A-T

Variant summary

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

The ENST00000562244.2(PWRN1):​n.403-9382A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0726 in 152,010 control chromosomes in the GnomAD database, including 806 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 0.073 (806 hom., cov: 32)
• Consequence: PWRN1 ENST00000562244.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.624
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370733	XR_007064536.1	n.874+3511A>G		intron_variant	Intron 1 of 6
LOC105370733	XR_007064537.1	n.795-26777A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PWRN1	ENST00000562244.2	n.403-9382A>G		intron_variant	Intron 4 of 11	3
PWRN1	ENST00000565295.6	n.426-9302A>G		intron_variant	Intron 2 of 14	3
PWRN1	ENST00000565512.6	n.111-26777A>G		intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.0725 AC: 11016 AN: 151892 Hom.: 800 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0404

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0288

Gnomad FIN AF: 0.0240

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0322

Gnomad OTH AF: 0.0594

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

GnomAD4 genome AF: 0.0726 AC: 11038 AN: 152010 Hom.: 806 Cov.: 32 AF XY: 0.0689 AC XY: 5121 AN XY: 74320

African (AFR) AF: 0.183 AC: 7562 AN: 41414

American (AMR) AF: 0.0404 AC: 616 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 112 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5170

South Asian (SAS) AF: 0.0286 AC: 138 AN: 4822

European-Finnish (FIN) AF: 0.0240 AC: 254 AN: 10592

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0323 AC: 2192 AN: 67964

Other (OTH) AF: 0.0583 AC: 123 AN: 2110

Alfa AF: 0.0481 Hom.: 48

Bravo AF: 0.0794

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.49
DANN	Benign	0.40
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs7496441; hg19: chr15-24727231;