Genetic Variant LAP3P2:n.1378C>T (chr6-36675194-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 ENST00000454686.1(LAP3P2):n.1378C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 1,437,586 control chromosomes in the GnomAD database, including 23,342 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 0.22 ( 4468 hom., cov: 32)

Exomes 𝑓: 0.15 ( 18874 hom. )

Consequence

LAP3P2
ENST00000454686.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.16

Publications

3 publications found

Variant links:

COSMIC-nc: COSV55190844

Genes affected

LAP3P2 (HGNC:42365): (leucine aminopeptidase 3 pseudogene 2)

LAP3P2 links:

PANDAR (HGNC:44048): (promoter of CDKN1A antisense DNA damage activated RNA) This gene produces a non-coding RNA that is thought to regulate the response to DNA damage. This gene is induced by tumor protein p53 and interacts with and modulates the activity of a transcription factor that induce pro-apoptotic genes. Deregulation of this gene is associated with cancer progression. [provided by RefSeq, Dec 2017]

PANDAR links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000454686.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.64).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000454686.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PANDAR	NR_109836.1		n.-68G>A		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LAP3P2	ENST00000454686.1	TSL:6	n.1378C>T		non_coding_transcript_exon	Exon 1 of 1
	PANDAR	ENST00000629595.1	TSL:6	n.-68G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes

AF:

0.218

AC:

33166

AN:

152046

Hom.:

4453

Cov.:

show subpopulations

Gnomad AFR

AF:

0.329

Gnomad AMI

AF:

0.143

Gnomad AMR

AF:

0.322

Gnomad ASJ

AF:

0.0956

Gnomad EAS

AF:

0.422

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.118

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.142

Gnomad OTH

AF:

0.218

GnomAD4 exome

AF:

0.147

AC:

189074

AN:

1285422

Hom.:

18874

Cov.:

AF XY:

0.145

AC XY:

94097

AN XY:

648090

show subpopulations

African (AFR)

AF:

0.316

AC:

9080

AN:

28732

American (AMR)

AF:

0.416

AC:

18108

AN:

43528

Ashkenazi Jewish (ASJ)

AF:

0.0912

AC:

2257

AN:

24736

East Asian (EAS)

AF:

0.467

AC:

17844

AN:

38190

South Asian (SAS)

AF:

0.109

AC:

9001

AN:

82462

European-Finnish (FIN)

AF:

0.112

AC:

5841

AN:

52250

Middle Eastern (MID)

AF:

0.168

AC:

884

AN:

5272

European-Non Finnish (NFE)

AF:

0.123

AC:

117728

AN:

956138

Other (OTH)

AF:

0.154

AC:

8331

AN:

54114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.437

Heterozygous variant carriers

6837

13675

20512

27350

34187

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4102

8204

12306

16408

20510

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.218

AC:

33225

AN:

152164

Hom.:

4468

Cov.:

AF XY:

0.219

AC XY:

16285

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.330

AC:

13679

AN:

41498

American (AMR)

AF:

0.322

AC:

4930

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0956

AC:

331

AN:

3462

East Asian (EAS)

AF:

0.422

AC:

2182

AN:

5176

South Asian (SAS)

AF:

0.121

AC:

586

AN:

4826

European-Finnish (FIN)

AF:

0.118

AC:

1251

AN:

10588

Middle Eastern (MID)

AF:

0.156

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.142

AC:

9631

AN:

68006

Other (OTH)

AF:

0.217

AC:

459

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1267

2534

3800

5067

6334

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

322

644

966

1288

1610

<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:

0.172

Hom.:

582

Bravo

AF:

0.246

Asia WGS

AF:

0.251

AC:

873

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

(source)

DANN

Benign

0.63

PhyloP100

2.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over