dbSNP rs2609998: PENK-AS1:n.694+975G>A (chr8-56447475-G-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.694+975G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,368 control chromosomes in the GnomAD database, including 12,037 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 0.39 ( 12037 hom., cov: 29)

Consequence

PENK-AS1
ENST00000518662.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.32

Publications

8 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=-0.8).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PENK-AS1	NR_125813.1 link	n.694+975G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PENK-AS1	ENST00000518662.5 link	n.694+975G>A	intron_variant	Intron 1 of 3	2
PENK-AS1	ENST00000662661.1 link	n.264+975G>A	intron_variant	Intron 1 of 4
PENK-AS1	ENST00000685796.1 link	n.657+975G>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.386

AC:

58318

AN:

151250

Hom.:

12029

Cov.:

show subpopulations

Gnomad AFR

AF:

0.243

Gnomad AMI

AF:

0.403

Gnomad AMR

AF:

0.357

Gnomad ASJ

AF:

0.492

Gnomad EAS

AF:

0.349

Gnomad SAS

AF:

0.467

Gnomad FIN

AF:

0.533

Gnomad MID

AF:

0.497

Gnomad NFE

AF:

0.446

Gnomad OTH

AF:

0.392

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

GnomAD4 genome

AF:

0.385

AC:

58347

AN:

151368

Hom.:

12037

Cov.:

AF XY:

0.388

AC XY:

28659

AN XY:

73870

show subpopulations

African (AFR)

AF:

0.243

AC:

10026

AN:

41280

American (AMR)

AF:

0.357

AC:

5432

AN:

15232

Ashkenazi Jewish (ASJ)

AF:

0.492

AC:

1707

AN:

3470

East Asian (EAS)

AF:

0.349

AC:

1762

AN:

5048

South Asian (SAS)

AF:

0.469

AC:

2237

AN:

4766

European-Finnish (FIN)

AF:

0.533

AC:

5575

AN:

10452

Middle Eastern (MID)

AF:

0.490

AC:

144

AN:

294

European-Non Finnish (NFE)

AF:

0.446

AC:

30275

AN:

67816

Other (OTH)

AF:

0.392

AC:

823

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.523

Heterozygous variant carriers

1711

3421

5132

6842

8553

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

552

1104

1656

2208

2760

<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:

0.412

Hom.:

1544

Bravo

AF:

0.366

Asia WGS

AF:

0.413

AC:

1440

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

8.6

(source)

DANN

Benign

0.85

PhyloP100

1.3

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