5-27466859-G-T

Variant names:

• chr5-27466859-G-T
• rs6864587
• ENST00000650981.1:n.645-5524G>T

Variant summary

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

The ENST00000650981.1(PURPL):​n.645-5524G>T variant causes a intron 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 ENST00000650981.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PURPL	ENST00000650981.1		n.645-5524G>T		intron	N/A
	PURPL	ENST00000651409.1		n.776-5524G>T		intron	N/A
	PURPL	ENST00000710963.1		n.491-5524G>T		intron	N/A

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

African (AFR) AF: 0.717 AC: 29716 AN: 41462

American (AMR) AF: 0.545 AC: 8304 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1852 AN: 3458

East Asian (EAS) AF: 0.203 AC: 1043 AN: 5126

South Asian (SAS) AF: 0.554 AC: 2672 AN: 4820

European-Finnish (FIN) AF: 0.515 AC: 5396 AN: 10470

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.606 AC: 41107 AN: 67804

Other (OTH) AF: 0.596 AC: 1255 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.040
DANN	Benign	0.18
PhyloP100		-1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6864587;

hg19: chr5-27466966;