5-27466859-G-T

Variant summary

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

The ENST00000651409.1(PURPL):n.776-5524G>T 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 0.607 in 151,684 control chromosomes in the GnomAD database, including 28,913 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 0.61 (28913 hom., cov: 31)
• Consequence: PURPL ENST00000651409.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 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.776-5524G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91887 AN: 151566 Hom.: 28863 Cov.: 31

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.607 AC: 91999 AN: 151684 Hom.: 28913 Cov.: 31 AF XY: 0.599 AC XY: 44347 AN XY: 74064

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.596

Alfa AF: 0.596 Hom.: 5378

Bravo AF: 0.612

Asia WGS AF: 0.407 AC: 1418 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.040
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6864587; hg19: chr5-27466966;