rs1021003

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

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.336-18931A>G		intron_variant	Intron 1 of 9
PURPL	ENST00000651409.1	n.621-18931A>G		intron_variant	Intron 1 of 8
PURPL	ENST00000710963.1	n.336-18931A>G		intron_variant	Intron 1 of 4

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

Gnomad4 AFR AF: 0.0468

Gnomad4 AMR AF: 0.0686

Gnomad4 ASJ AF: 0.0848

Gnomad4 EAS AF: 0.00290

Gnomad4 SAS AF: 0.0915

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.0900

Alfa AF: 0.109 Hom.: 112

Bravo AF: 0.0834

Asia WGS AF: 0.0430 AC: 149 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1021003; hg19: chr5-27262189;