rs9920573

Positions:

• chr15-24543194-T-C

Variant summary

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

The variant allele was found at a frequency of 0.425 in 151,952 control chromosomes in the GnomAD database, including 13,816 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 0.43 (13816 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.33

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.24543194T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PWRN1	ENST00000565295.6	n.1612-2869T>C		intron_variant		3
PWRN1	ENST00000568045.6	n.944+7388T>C		intron_variant		2
PWRN1	ENST00000651815.1	n.975-4136T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64570 AN: 151834 Hom.: 13808 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.425 AC: 64597 AN: 151952 Hom.: 13816 Cov.: 32 AF XY: 0.422 AC XY: 31370 AN XY: 74264

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.407

Alfa AF: 0.413 Hom.: 2166

Bravo AF: 0.426

Asia WGS AF: 0.391 AC: 1361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.28
DANN	Benign	0.042

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9920573; hg19: chr15-24788341;