chr5-1323081-T-C

Variant names:

• chr5-1323081-T-C
• rs410805
• NM_030782.5:c.1281-170A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030782.5(CLPTM1L):​c.1281-170A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.856 in 152,228 control chromosomes in the GnomAD database, including 56,248 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 0.86 (56248 hom., cov: 37)
• Consequence: CLPTM1L NM_030782.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.955 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.1281-170A>G		intron	N/A	NP_110409.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLPTM1L	ENST00000320895.10	TSL:1 MANE Select	c.1281-170A>G		intron	N/A	ENSP00000313854.5	Q96KA5-1
	CLPTM1L	ENST00000507807.3	TSL:1	c.774-170A>G		intron	N/A	ENSP00000423321.1	G5E9Z2
	CLPTM1L	ENST00000966757.1		c.1485-170A>G		intron	N/A	ENSP00000636816.1

Frequencies

GnomAD3 genomes AF: 0.856 AC: 130222 AN: 152110 Hom.: 56198 Cov.: 37

Gnomad AFR AF: 0.963

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.856 AC: 130327 AN: 152228 Hom.: 56248 Cov.: 37 AF XY: 0.853 AC XY: 63478 AN XY: 74418

African (AFR) AF: 0.963 AC: 40013 AN: 41560

American (AMR) AF: 0.812 AC: 12430 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2753 AN: 3472

East Asian (EAS) AF: 0.673 AC: 3483 AN: 5176

South Asian (SAS) AF: 0.728 AC: 3514 AN: 4824

European-Finnish (FIN) AF: 0.854 AC: 9044 AN: 10588

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56357 AN: 67988

Other (OTH) AF: 0.829 AC: 1753 AN: 2114

Alfa AF: 0.856 Hom.: 6965

Bravo AF: 0.861

Asia WGS AF: 0.727 AC: 2519 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.26
PhyloP100		-0.24
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: rs410805; hg19: chr5-1323196;