rs31489

chr5-1342599-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030782.5(CLPTM1L):c.264-739G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 152,072 control chromosomes in the GnomAD database, including 13,051 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 (13051 hom., cov: 33)
• Consequence: CLPTM1L NM_030782.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLPTM1L	NM_030782.5	c.264-739G>T		intron_variant		ENST00000320895.10
CLPTM1L	XM_011514144.3	c.264-739G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLPTM1L	ENST00000320895.10	c.264-739G>T		intron_variant		1	NM_030782.5	P1
CLPTM1L	ENST00000630539.1	c.-136-739G>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61733 AN: 151954 Hom.: 13040 Cov.: 33

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.406 AC: 61789 AN: 152072 Hom.: 13051 Cov.: 33 AF XY: 0.400 AC XY: 29737 AN XY: 74336

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.395

Alfa AF: 0.398 Hom.: 22874

Bravo AF: 0.403

Asia WGS AF: 0.216 AC: 753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.4
Dann	Benign	0.64

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

Other links and lift over

dbSNP: rs31489; hg19: chr5-1342714;