5-1317834-C-T

Variant names:

• chr5-1317834-C-T
• rs1801075
• NM_030782.5:c.*535G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -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.

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.*535G>A		3_prime_UTR	Exon 17 of 17	NP_110409.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLPTM1L	ENST00000320895.10	TSL:1 MANE Select	c.*535G>A		3_prime_UTR	Exon 17 of 17	ENSP00000313854.5
	CLPTM1L	ENST00000507807.3	TSL:1	c.*535G>A		3_prime_UTR	Exon 14 of 14	ENSP00000423321.1
	CLPTM1L	ENST00000879373.1		c.*535G>A		3_prime_UTR	Exon 17 of 17	ENSP00000549432.1

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

African (AFR) AF: 0.875 AC: 14 AN: 16

American (AMR) AF: 0.833 AC: 5 AN: 6

Ashkenazi Jewish (ASJ) AF: 0.917 AC: 11 AN: 12

East Asian (EAS) AF: 1.00 AC: 14 AN: 14

South Asian (SAS) AF: 1.00 AC: 4 AN: 4

European-Finnish (FIN) AF: 0.600 AC: 6 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.806 AC: 200 AN: 248

Other (OTH) AF: 0.792 AC: 19 AN: 24

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

African (AFR) AF: 0.838 AC: 34812 AN: 41520

American (AMR) AF: 0.868 AC: 13281 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2714 AN: 3472

East Asian (EAS) AF: 0.949 AC: 4929 AN: 5192

South Asian (SAS) AF: 0.925 AC: 4471 AN: 4832

European-Finnish (FIN) AF: 0.773 AC: 8181 AN: 10582

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56144 AN: 68014

Other (OTH) AF: 0.836 AC: 1768 AN: 2114

Alfa AF: 0.830 Hom.: 198882

Bravo AF: 0.843

Asia WGS AF: 0.924 AC: 3212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.36
PhyloP100		-0.12
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1801075; hg19: chr5-1317949;