rs10520934

chr5-27384877-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000651409.1(PURPL):n.700-22166G>A 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 0.0132 in 151,980 control chromosomes in the GnomAD database, including 23 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 0.013 (23 hom., cov: 32)
• Consequence: PURPL ENST00000651409.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158

Genes affected

PURPL (HGNC:48995): (p53 upregulated regulator of p53 levels)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0132 (2005/151980) while in subpopulation AMR AF= 0.0177 (269/15216). AF 95% confidence interval is 0.0159. There are 23 homozygotes in gnomad4. There are 998 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 23 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PURPL	ENST00000651409.1	n.700-22166G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0132 AC: 2005 AN: 151862 Hom.: 23 Cov.: 32

Gnomad AFR AF: 0.00790

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0177

Gnomad ASJ AF: 0.0231

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00415

Gnomad FIN AF: 0.0227

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0151

Gnomad OTH AF: 0.0139

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

GnomAD4 genome AF: 0.0132 AC: 2005 AN: 151980 Hom.: 23 Cov.: 32 AF XY: 0.0134 AC XY: 998 AN XY: 74280

Gnomad4 AFR AF: 0.00787

Gnomad4 AMR AF: 0.0177

Gnomad4 ASJ AF: 0.0231

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00415

Gnomad4 FIN AF: 0.0227

Gnomad4 NFE AF: 0.0151

Gnomad4 OTH AF: 0.0138

Alfa AF: 0.0142 Hom.: 5

Bravo AF: 0.0132

Asia WGS AF: 0.00261 AC: 9 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.61
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520934; hg19: chr5-27384984; COSMIC: COSV67310660;