Genetic Variant PENK-AS1:n.695-23786C>A (chr8-56472437-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000518662.5(PENK-AS1):n.695-23786C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 151,862 control chromosomes in the GnomAD database, including 15,313 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 0.45 ( 15313 hom., cov: 31)

Consequence

PENK-AS1
ENST00000518662.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.64

Publications

1 publications found

Variant links:

Genes affected

PENK-AS1 (HGNC:55519): (PENK antisense RNA 1)

PENK-AS1 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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PENK-AS1	NR_125813.1 link	n.695-23786C>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PENK-AS1	ENST00000518662.5 link	n.695-23786C>A	intron_variant	Intron 1 of 3	2
PENK-AS1	ENST00000662661.1 link	n.265-23786C>A	intron_variant	Intron 1 of 4
PENK-AS1	ENST00000685796.1 link	n.658-23786C>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.445

AC:

67587

AN:

151744

Hom.:

15286

Cov.:

show subpopulations

Gnomad AFR

AF:

0.516

Gnomad AMI

AF:

0.404

Gnomad AMR

AF:

0.376

Gnomad ASJ

AF:

0.499

Gnomad EAS

AF:

0.296

Gnomad SAS

AF:

0.438

Gnomad FIN

AF:

0.506

Gnomad MID

AF:

0.519

Gnomad NFE

AF:

0.419

Gnomad OTH

AF:

0.437

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

GnomAD4 genome

AF:

0.446

AC:

67655

AN:

151862

Hom.:

15313

Cov.:

AF XY:

0.446

AC XY:

33115

AN XY:

74206

show subpopulations

African (AFR)

AF:

0.516

AC:

21360

AN:

41416

American (AMR)

AF:

0.376

AC:

5737

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.499

AC:

1733

AN:

3472

East Asian (EAS)

AF:

0.296

AC:

1521

AN:

5136

South Asian (SAS)

AF:

0.440

AC:

2117

AN:

4812

European-Finnish (FIN)

AF:

0.506

AC:

5325

AN:

10530

Middle Eastern (MID)

AF:

0.514

AC:

151

AN:

294

European-Non Finnish (NFE)

AF:

0.419

AC:

28427

AN:

67918

Other (OTH)

AF:

0.435

AC:

916

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1840

3680

5521

7361

9201

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

606

1212

1818

2424

3030

<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:

0.444

Hom.:

1899

Bravo

AF:

0.438

Asia WGS

AF:

0.385

AC:

1344

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.047

(source)

DANN

Benign

0.45

PhyloP100

-3.6

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