dbSNP rs4421076: PURPL:n.644+9226A>G (chr5-27447756-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13

Publications

2 publications found

Variant links:

Genes affected

PURPL (HGNC:48995): (p53 upregulated regulator of p53 levels)

PURPL links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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	Effect	Exon rank
PURPL	ENST00000650981.1 link	n.644+9226A>G	intron_variant	Intron 4 of 9
PURPL	ENST00000651409.1 link	n.776-24627A>G	intron_variant	Intron 3 of 8
PURPL	ENST00000710963.1 link	n.491-24627A>G	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.616

AC:

93499

AN:

151880

Hom.:

30010

Cov.:

show subpopulations

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.:

AF XY:

0.607

AC XY:

45085

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.758

AC:

31444

AN:

41466

American (AMR)

AF:

0.539

AC:

8237

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.533

AC:

1850

AN:

3472

East Asian (EAS)

AF:

0.206

AC:

1058

AN:

5146

South Asian (SAS)

AF:

0.554

AC:

2671

AN:

4818

European-Finnish (FIN)

AF:

0.514

AC:

5423

AN:

10556

Middle Eastern (MID)

AF:

0.571

AC:

168

AN:

294

European-Non Finnish (NFE)

AF:

0.604

AC:

41034

AN:

67950

Other (OTH)

AF:

0.603

AC:

1272

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1716

3431

5147

6862

8578

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

760

1520

2280

3040

3800

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.606

Hom.:

90733

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

(source)

DANN

Benign

0.40

PhyloP100

-1.1

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over