rs8026512

Variant names:

• chr15-24012512-T-C
• rs8026512
• ENST00000652183.1:n.784+33301T>C

Your query was ambiguous. Multiple possible variants found:

• chr15-24012512-T-C
• chr15-24012512-T-G

Variant summary

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

The NR_126392.1(PWRN4):​n.445+9077T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,808 control chromosomes in the GnomAD database, including 7,968 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 0.32 (7968 hom., cov: 31)
• Consequence: PWRN4 NR_126392.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 4 publications found

Genes affected

PWRN4 (HGNC:49130): (Prader-Willi region non-protein coding RNA 4)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_126392.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PWRN4	NR_126392.1		n.445+9077T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PWRN4	ENST00000652183.1		n.784+33301T>C		intron	N/A
	PWRN4	ENST00000661343.1		n.487+33301T>C		intron	N/A
	PWRN4	ENST00000663707.1		n.435+33301T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48500 AN: 151690 Hom.: 7957 Cov.: 31

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.320 AC: 48534 AN: 151808 Hom.: 7968 Cov.: 31 AF XY: 0.313 AC XY: 23207 AN XY: 74164

African (AFR) AF: 0.321 AC: 13298 AN: 41382

American (AMR) AF: 0.269 AC: 4094 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 983 AN: 3464

East Asian (EAS) AF: 0.170 AC: 874 AN: 5150

South Asian (SAS) AF: 0.285 AC: 1367 AN: 4804

European-Finnish (FIN) AF: 0.268 AC: 2827 AN: 10538

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.356 AC: 24174 AN: 67918

Other (OTH) AF: 0.298 AC: 630 AN: 2112

Alfa AF: 0.339 Hom.: 24891

Bravo AF: 0.319

Asia WGS AF: 0.234 AC: 812 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.62
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs8026512; hg19: chr15-24257659;