Genetic Variant PRR15-DT:n.425+6428G>A (chr7-29592311-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+6428G>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 152,120 control chromosomes in the GnomAD database, including 1,171 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 ( 1171 hom., cov: 32)

Consequence

PRR15-DT
ENST00000748764.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0700

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=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 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+6428G>A	intron_variant	Intron 3 of 5
PRR15-DT	ENST00000748765.1 link	n.424+6428G>A	intron_variant	Intron 3 of 6
PRR15-DT	ENST00000748766.1 link	n.408+6428G>A	intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

16658

AN:

152002

Hom.:

1168

Cov.:

show subpopulations

Gnomad AFR

AF:

0.190

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.0556

Gnomad ASJ

AF:

0.0806

Gnomad EAS

AF:

0.217

Gnomad SAS

AF:

0.0995

Gnomad FIN

AF:

0.0931

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.0712

Gnomad OTH

AF:

0.0924

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

GnomAD4 genome

AF:

0.110

AC:

16671

AN:

152120

Hom.:

1171

Cov.:

AF XY:

0.110

AC XY:

8154

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.190

AC:

7886

AN:

41470

American (AMR)

AF:

0.0554

AC:

848

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0806

AC:

280

AN:

3472

East Asian (EAS)

AF:

0.216

AC:

1118

AN:

5164

South Asian (SAS)

AF:

0.0992

AC:

478

AN:

4820

European-Finnish (FIN)

AF:

0.0931

AC:

986

AN:

10586

Middle Eastern (MID)

AF:

0.0986

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0712

AC:

4844

AN:

67996

Other (OTH)

AF:

0.0915

AC:

193

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

744

1488

2233

2977

3721

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

360

540

720

900

<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:

0.0719

Hom.:

252

Bravo

AF:

0.111

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.4

(source)

DANN

Benign

0.37

PhyloP100

-0.070

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