5-1317834-C-T

Position:

• chr5-1317834-C-T

Variant summary

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

The NM_030782.5(CLPTM1L):​c.*535G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,564 control chromosomes in the GnomAD database, including 53,407 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 0.84 (53293 hom., cov: 33)
  • Exomes 𝑓: 0.82 (114 hom.)
• Consequence: CLPTM1L NM_030782.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLPTM1L	NM_030782.5	c.*535G>A		3_prime_UTR_variant	17/17	ENST00000320895.10	NP_110409.2
CLPTM1L	XM_011514144.3	c.*535G>A		3_prime_UTR_variant	17/17		XP_011512446.1
CLPTM1L	XM_024446222.2	c.*535G>A		3_prime_UTR_variant	15/15		XP_024301990.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLPTM1L	ENST00000320895	c.*535G>A		3_prime_UTR_variant	17/17	1	NM_030782.5	ENSP00000313854.5
CLPTM1L	ENST00000507807	c.*535G>A		3_prime_UTR_variant	14/14	1		ENSP00000423321.1
CLPTM1L	ENST00000503042.5	n.*34G>A		downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127160 AN: 152112 Hom.: 53256 Cov.: 33

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.837

GnomAD4 exome AF: 0.817 AC: 273 AN: 334 Hom.: 114 Cov.: 0 AF XY: 0.849 AC XY: 141 AN XY: 166

Gnomad4 AFR exome AF: 0.875

Gnomad4 AMR exome AF: 0.833

Gnomad4 ASJ exome AF: 0.917

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.600

Gnomad4 NFE exome AF: 0.806

Gnomad4 OTH exome AF: 0.792

GnomAD4 genome AF: 0.836 AC: 127255 AN: 152230 Hom.: 53293 Cov.: 33 AF XY: 0.836 AC XY: 62253 AN XY: 74426

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.782

Gnomad4 EAS AF: 0.949

Gnomad4 SAS AF: 0.925

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.825

Gnomad4 OTH AF: 0.836

Alfa AF: 0.828 Hom.: 86893

Bravo AF: 0.843

Asia WGS AF: 0.924 AC: 3212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.36
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

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: rs1801075; hg19: chr5-1317949;