dbSNP rs715301: PRR15-DT:n.425+23014G>A (chr7-29575725-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000748764.1(PRR15-DT):n.425+23014G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,140 control chromosomes in the GnomAD database, including 1,129 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 0.11 ( 1129 hom., cov: 32)

Consequence

PRR15-DT
ENST00000748764.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.273

Publications

2 publications found

Variant links:

Genes affected

PRR15-DT (HGNC:55866): (PRR15 divergent transcript)

PRR15-DT 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
PRR15-DT	ENST00000748764.1 link	n.425+23014G>A	intron_variant	Intron 3 of 5
PRR15-DT	ENST00000748765.1 link	n.424+23014G>A	intron_variant	Intron 3 of 6
PRR15-DT	ENST00000748766.1 link	n.408+23014G>A	intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

16658

AN:

152022

Hom.:

1128

Cov.:

show subpopulations

Gnomad AFR

AF:

0.186

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.0562

Gnomad ASJ

AF:

0.0804

Gnomad EAS

AF:

0.220

Gnomad SAS

AF:

0.0978

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0725

Gnomad OTH

AF:

0.0915

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

GnomAD4 genome

AF:

0.110

AC:

16665

AN:

152140

Hom.:

1129

Cov.:

AF XY:

0.110

AC XY:

8181

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.186

AC:

7694

AN:

41458

American (AMR)

AF:

0.0561

AC:

858

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0804

AC:

279

AN:

3472

East Asian (EAS)

AF:

0.220

AC:

1137

AN:

5172

South Asian (SAS)

AF:

0.0975

AC:

470

AN:

4820

European-Finnish (FIN)

AF:

0.101

AC:

1070

AN:

10598

Middle Eastern (MID)

AF:

0.0952

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0725

AC:

4929

AN:

67998

Other (OTH)

AF:

0.0905

AC:

191

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

750

1500

2249

2999

3749

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

182

364

546

728

910

<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:

0.101

Hom.:

108

Bravo

AF:

0.111

Asia WGS

AF:

0.184

AC:

640

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

7.6

(source)

DANN

Benign

0.38

PhyloP100

0.27

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