chr5-27262082-A-G

Variant names:

• chr5-27262082-A-G
• rs1021003
• ENST00000650981.1:n.336-18931A>G

Variant summary

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

The ENST00000650981.1(PURPL):​n.336-18931A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0902 in 152,238 control chromosomes in the GnomAD database, including 726 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 0.090 (726 hom., cov: 32)
• Consequence: PURPL ENST00000650981.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.672
• Publications: 1 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650981.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PURPL	ENST00000650981.1		n.336-18931A>G		intron	N/A
	PURPL	ENST00000651409.1		n.621-18931A>G		intron	N/A
	PURPL	ENST00000710963.1		n.336-18931A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0903 AC: 13740 AN: 152120 Hom.: 725 Cov.: 32

Gnomad AFR AF: 0.0470

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.0687

Gnomad ASJ AF: 0.0848

Gnomad EAS AF: 0.00309

Gnomad SAS AF: 0.0921

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.0914

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

GnomAD4 genome AF: 0.0902 AC: 13733 AN: 152238 Hom.: 726 Cov.: 32 AF XY: 0.0892 AC XY: 6635 AN XY: 74422

African (AFR) AF: 0.0468 AC: 1947 AN: 41568

American (AMR) AF: 0.0686 AC: 1049 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0848 AC: 294 AN: 3466

East Asian (EAS) AF: 0.00290 AC: 15 AN: 5174

South Asian (SAS) AF: 0.0915 AC: 442 AN: 4830

European-Finnish (FIN) AF: 0.124 AC: 1311 AN: 10576

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8377 AN: 68008

Other (OTH) AF: 0.0900 AC: 190 AN: 2112

Alfa AF: 0.106 Hom.: 112

Bravo AF: 0.0834

Asia WGS AF: 0.0430 AC: 149 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.1
DANN	Benign	0.84
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs1021003; hg19: chr5-27262189;