rs4421076

Variant names:

• chr5-27447756-A-G
• rs4421076
• ENST00000650981.1:n.644+9226A>G

Variant summary

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

The ENST00000650981.1(PURPL):​n.644+9226A>G variant causes a intron 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 ENST00000650981.1 intron
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PURPL	ENST00000650981.1	n.644+9226A>G		intron_variant	Intron 4 of 9
PURPL	ENST00000651409.1	n.776-24627A>G		intron_variant	Intron 3 of 8
PURPL	ENST00000710963.1	n.491-24627A>G		intron_variant	Intron 3 of 4

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;