Genetic Variant CLPTM1L:c.1316-153G>A (chr5-1321972-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 NM_030782.5(CLPTM1L):c.1316-153G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 704,354 control chromosomes in the GnomAD database, including 67,106 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 0.47 ( 17548 hom., cov: 34)

Exomes 𝑓: 0.41 ( 49558 hom. )

Consequence

CLPTM1L
NM_030782.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.26

Publications

337 publications found

Variant links:

Genes affected

CLPTM1L (HGNC:24308): (CLPTM1 like) The protein encoded by this gene is a membrane protein whose overexpression in cisplatin-sensitive cells causes apoptosis. Polymorphisms in this gene have been reported to increase susceptibility to several cancers, including lung, pancreatic, and breast cancers. [provided by RefSeq, Nov 2015]

CLPTM1L links:

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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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030782.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLPTM1L	NM_030782.5	MANE Select	c.1316-153G>A		intron	N/A	NP_110409.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CLPTM1L	ENST00000320895.10	TSL:1 MANE Select	c.1316-153G>A	intron	N/A	ENSP00000313854.5
CLPTM1L	ENST00000507807.3	TSL:1	c.809-153G>A	intron	N/A	ENSP00000423321.1
CLPTM1L	ENST00000966757.1		c.1520-153G>A	intron	N/A	ENSP00000636816.1

Frequencies

GnomAD3 genomes

AF:

0.472

AC:

71708

AN:

151958

Hom.:

17526

Cov.:

show subpopulations

Gnomad AFR

AF:

0.593

Gnomad AMI

AF:

0.474

Gnomad AMR

AF:

0.433

Gnomad ASJ

AF:

0.449

Gnomad EAS

AF:

0.319

Gnomad SAS

AF:

0.214

Gnomad FIN

AF:

0.494

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.435

Gnomad OTH

AF:

0.452

GnomAD4 exome

AF:

0.414

AC:

228381

AN:

552278

Hom.:

49558

AF XY:

0.402

AC XY:

117952

AN XY:

293754

show subpopulations

African (AFR)

AF:

0.593

AC:

8949

AN:

15098

American (AMR)

AF:

0.406

AC:

12172

AN:

29972

Ashkenazi Jewish (ASJ)

AF:

0.434

AC:

7481

AN:

17228

East Asian (EAS)

AF:

0.331

AC:

10573

AN:

31944

South Asian (SAS)

AF:

0.205

AC:

11370

AN:

55560

European-Finnish (FIN)

AF:

0.492

AC:

22899

AN:

46556

Middle Eastern (MID)

AF:

0.404

AC:

927

AN:

2292

European-Non Finnish (NFE)

AF:

0.436

AC:

141160

AN:

323934

Other (OTH)

AF:

0.433

AC:

12850

AN:

29694

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

7877

15754

23632

31509

39386

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1028

2056

3084

4112

5140

<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:

0.472

AC:

71787

AN:

152076

Hom.:

17548

Cov.:

AF XY:

0.467

AC XY:

34746

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.593

AC:

24593

AN:

41472

American (AMR)

AF:

0.433

AC:

6618

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.449

AC:

1558

AN:

3470

East Asian (EAS)

AF:

0.319

AC:

1650

AN:

5170

South Asian (SAS)

AF:

0.213

AC:

1028

AN:

4824

European-Finnish (FIN)

AF:

0.494

AC:

5230

AN:

10580

Middle Eastern (MID)

AF:

0.449

AC:

132

AN:

294

European-Non Finnish (NFE)

AF:

0.435

AC:

29599

AN:

67972

Other (OTH)

AF:

0.451

AC:

948

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1904

3808

5711

7615

9519

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

630

1260

1890

2520

3150

<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.:

52684

Bravo

AF:

0.480

Asia WGS

AF:

0.290

AC:

1009

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.16

(source)

DANN

Benign

0.39

PhyloP100

-3.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over