5-27448697-A-G

Variant names:

• chr5-27448697-A-G
• rs10039598
• ENST00000650981.1:n.644+10167A>G

Variant summary

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

The ENST00000650981.1(PURPL):​n.644+10167A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 151,934 control chromosomes in the GnomAD database, including 27,577 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 0.59 (27577 hom., cov: 31)
• Consequence: PURPL ENST00000650981.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 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.644+10167A>G		intron	N/A
	PURPL	ENST00000651409.1		n.776-23686A>G		intron	N/A
	PURPL	ENST00000710963.1		n.491-23686A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.593 AC: 89993 AN: 151816 Hom.: 27532 Cov.: 31

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.593 AC: 90099 AN: 151934 Hom.: 27577 Cov.: 31 AF XY: 0.585 AC XY: 43414 AN XY: 74262

African (AFR) AF: 0.681 AC: 28224 AN: 41436

American (AMR) AF: 0.531 AC: 8097 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1818 AN: 3472

East Asian (EAS) AF: 0.205 AC: 1055 AN: 5142

South Asian (SAS) AF: 0.553 AC: 2661 AN: 4816

European-Finnish (FIN) AF: 0.514 AC: 5432 AN: 10566

Middle Eastern (MID) AF: 0.556 AC: 160 AN: 288

European-Non Finnish (NFE) AF: 0.603 AC: 40968 AN: 67936

Other (OTH) AF: 0.583 AC: 1229 AN: 2108

Alfa AF: 0.505 Hom.: 2380

Bravo AF: 0.598

Asia WGS AF: 0.408 AC: 1422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.65
DANN	Benign	0.23
PhyloP100		-1.4

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: rs10039598;

hg19: chr5-27448804;