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GeneBe

rs401681

Variant summary

Our verdict is Benign. Variant got -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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.26
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CLPTM1LNM_030782.5 linkuse as main transcriptc.1316-153G>A intron_variant ENST00000320895.10
CLPTM1LXM_011514144.3 linkuse as main transcriptc.1313-153G>A intron_variant
CLPTM1LXM_024446222.2 linkuse as main transcriptc.782-153G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CLPTM1LENST00000320895.10 linkuse as main transcriptc.1316-153G>A intron_variant 1 NM_030782.5 P1Q96KA5-1

Frequencies

GnomAD3 genomes
AF:
0.472
AC:
71708
AN:
151958
Hom.:
17526
Cov.:
34
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
Gnomad4 AFR exome
AF:
0.593
Gnomad4 AMR exome
AF:
0.406
Gnomad4 ASJ exome
AF:
0.434
Gnomad4 EAS exome
AF:
0.331
Gnomad4 SAS exome
AF:
0.205
Gnomad4 FIN exome
AF:
0.492
Gnomad4 NFE exome
AF:
0.436
Gnomad4 OTH exome
AF:
0.433
GnomAD4 genome
AF:
0.472
AC:
71787
AN:
152076
Hom.:
17548
Cov.:
34
AF XY:
0.467
AC XY:
34746
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.593
Gnomad4 AMR
AF:
0.433
Gnomad4 ASJ
AF:
0.449
Gnomad4 EAS
AF:
0.319
Gnomad4 SAS
AF:
0.213
Gnomad4 FIN
AF:
0.494
Gnomad4 NFE
AF:
0.435
Gnomad4 OTH
AF:
0.451
Alfa
AF:
0.433
Hom.:
17929
Bravo
AF:
0.480
Asia WGS
AF:
0.290
AC:
1009
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
Cadd
Benign
0.16
Dann
Benign
0.39

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs401681; hg19: chr5-1322087; COSMIC: COSV57990702; COSMIC: COSV57990702; API