rs4421076

chr5-27447756-A-G

Variant summary

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

The ENST00000651409.1(PURPL):n.776-24627A>G 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 0.616 in 152,000 control chromosomes in the GnomAD database, including 30,061 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 0.62 (30061 hom., cov: 32)
• Consequence: PURPL ENST00000651409.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

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.776-24627A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93499 AN: 151880 Hom.: 30010 Cov.: 32

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.616 AC: 93612 AN: 152000 Hom.: 30061 Cov.: 32 AF XY: 0.607 AC XY: 45085 AN XY: 74284

Gnomad4 AFR AF: 0.758

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.603

Alfa AF: 0.598 Hom.: 55824

Bravo AF: 0.623

Asia WGS AF: 0.414 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4421076; hg19: chr5-27447863;