rs10520934

Variant names:

• chr5-27384877-G-A
• rs10520934
• ENST00000650981.1:n.415-22166G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000650981.1(PURPL):​n.415-22166G>A variant causes a intron 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 ENST00000650981.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 23 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PURPL	ENST00000650981.1	n.415-22166G>A		intron_variant	Intron 2 of 9
PURPL	ENST00000651409.1	n.700-22166G>A		intron_variant	Intron 2 of 8
PURPL	ENST00000710963.1	n.415-22166G>A		intron_variant	Intron 2 of 4

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

African (AFR) AF: 0.00787 AC: 327 AN: 41534

American (AMR) AF: 0.0177 AC: 269 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.0231 AC: 80 AN: 3466

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5176

South Asian (SAS) AF: 0.00415 AC: 20 AN: 4820

European-Finnish (FIN) AF: 0.0227 AC: 240 AN: 10584

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0151 AC: 1026 AN: 67874

Other (OTH) AF: 0.0138 AC: 29 AN: 2106

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
PhyloP100		-0.16

Splicing

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

Other links and lift over

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