dbSNP rs414965: CLPTM1L:c.1198-137C>T (chr5-1324006-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 NM_030782.5(CLPTM1L):c.1198-137C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 683,080 control chromosomes in the GnomAD database, including 51,471 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 0.41 ( 13174 hom., cov: 33)

Exomes 𝑓: 0.37 ( 38297 hom. )

Consequence

CLPTM1L
NM_030782.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.179

Publications

15 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLPTM1L	NM_030782.5	MANE Select	c.1198-137C>T		intron	N/A	NP_110409.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CLPTM1L	ENST00000320895.10	TSL:1 MANE Select	c.1198-137C>T	intron	N/A	ENSP00000313854.5	Q96KA5-1
CLPTM1L	ENST00000507807.3	TSL:1	c.691-137C>T	intron	N/A	ENSP00000423321.1	G5E9Z2
CLPTM1L	ENST00000966757.1		c.1402-137C>T	intron	N/A	ENSP00000636816.1

Frequencies

GnomAD3 genomes

AF:

0.408

AC:

62038

AN:

151912

Hom.:

13163

Cov.:

show subpopulations

Gnomad AFR

AF:

0.486

Gnomad AMI

AF:

0.475

Gnomad AMR

AF:

0.311

Gnomad ASJ

AF:

0.406

Gnomad EAS

AF:

0.180

Gnomad SAS

AF:

0.196

Gnomad FIN

AF:

0.446

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.409

Gnomad OTH

AF:

0.395

GnomAD4 exome

AF:

0.366

AC:

194577

AN:

531050

Hom.:

38297

Cov.:

AF XY:

0.357

AC XY:

100674

AN XY:

281652

show subpopulations

African (AFR)

AF:

0.489

AC:

7252

AN:

14830

American (AMR)

AF:

0.225

AC:

6594

AN:

29274

Ashkenazi Jewish (ASJ)

AF:

0.389

AC:

6518

AN:

16762

East Asian (EAS)

AF:

0.157

AC:

4991

AN:

31706

South Asian (SAS)

AF:

0.196

AC:

10620

AN:

54266

European-Finnish (FIN)

AF:

0.448

AC:

15334

AN:

34264

Middle Eastern (MID)

AF:

0.361

AC:

836

AN:

2318

European-Non Finnish (NFE)

AF:

0.412

AC:

131140

AN:

318464

Other (OTH)

AF:

0.387

AC:

11292

AN:

29166

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

5917

11834

17751

23668

29585

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

976

1952

2928

3904

4880

<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:

0.408

AC:

62094

AN:

152030

Hom.:

13174

Cov.:

AF XY:

0.402

AC XY:

29881

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.486

AC:

20161

AN:

41468

American (AMR)

AF:

0.311

AC:

4753

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.406

AC:

1408

AN:

3468

East Asian (EAS)

AF:

0.181

AC:

928

AN:

5140

South Asian (SAS)

AF:

0.196

AC:

944

AN:

4828

European-Finnish (FIN)

AF:

0.446

AC:

4719

AN:

10572

Middle Eastern (MID)

AF:

0.429

AC:

126

AN:

294

European-Non Finnish (NFE)

AF:

0.409

AC:

27794

AN:

67958

Other (OTH)

AF:

0.393

AC:

829

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1841

3683

5524

7366

9207

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

570

1140

1710

2280

2850

<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:

0.415

Hom.:

2235

Bravo

AF:

0.405

Asia WGS

AF:

0.219

AC:

767

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.5

(source)

DANN

Benign

0.54

PhyloP100

-0.18

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

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