dbSNP rs1021003: PURPL:n.336-18931A>G (chr5-27262082-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.336-18931A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0902 in 152,238 control chromosomes in the GnomAD database, including 726 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 0.090 ( 726 hom., cov: 32)

Consequence

PURPL
ENST00000650981.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.672

Publications

1 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=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 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.336-18931A>G	intron_variant	Intron 1 of 9
PURPL	ENST00000651409.1 link	n.621-18931A>G	intron_variant	Intron 1 of 8
PURPL	ENST00000710963.1 link	n.336-18931A>G	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.0903

AC:

13740

AN:

152120

Hom.:

725

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0470

Gnomad AMI

AF:

0.0932

Gnomad AMR

AF:

0.0687

Gnomad ASJ

AF:

0.0848

Gnomad EAS

AF:

0.00309

Gnomad SAS

AF:

0.0921

Gnomad FIN

AF:

0.124

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.0914

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

GnomAD4 genome

AF:

0.0902

AC:

13733

AN:

152238

Hom.:

726

Cov.:

AF XY:

0.0892

AC XY:

6635

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.0468

AC:

1947

AN:

41568

American (AMR)

AF:

0.0686

AC:

1049

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0848

AC:

294

AN:

3466

East Asian (EAS)

AF:

0.00290

AC:

AN:

5174

South Asian (SAS)

AF:

0.0915

AC:

442

AN:

4830

European-Finnish (FIN)

AF:

0.124

AC:

1311

AN:

10576

Middle Eastern (MID)

AF:

0.0782

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.123

AC:

8377

AN:

68008

Other (OTH)

AF:

0.0900

AC:

190

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

646

1293

1939

2586

3232

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

320

480

640

800

<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:

0.106

Hom.:

112

Bravo

AF:

0.0834

Asia WGS

AF:

0.0430

AC:

149

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.1

(source)

DANN

Benign

0.84

PhyloP100

0.67

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