Genetic Variant PURPL:n.645-5524G>T (chr5-27466859-G-T) – 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.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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.74

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=-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
PURPL	ENST00000650981.1 link	n.645-5524G>T	intron_variant	Intron 4 of 9
PURPL	ENST00000651409.1 link	n.776-5524G>T	intron_variant	Intron 3 of 8
PURPL	ENST00000710963.1 link	n.491-5524G>T	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.606

AC:

91887

AN:

151566

Hom.:

28863

Cov.:

show subpopulations

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.:

AF XY:

0.599

AC XY:

44347

AN XY:

74064

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1746

3492

5239

6985

8731

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

754

1508

2262

3016

3770

<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:

0.596

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

(source)

DANN

Benign

0.18

PhyloP100

-1.7

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