rs402710

Variant names:

• chr5-1320607-C-G
• rs402710
• NM_030782.5:c.1532+9G>C

Your query was ambiguous. Multiple possible variants found:

• chr5-1320607-C-G
• chr5-1320607-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_030782.5(CLPTM1L):​c.1532+9G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000743 in 1,345,936 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 34)
  • Exomes 𝑓: 7.4e-7 (0 hom.)
• Consequence: CLPTM1L NM_030782.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLPTM1L	NM_030782.5	MANE Select	c.1532+9G>C		intron	N/A	NP_110409.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLPTM1L	ENST00000320895.10	TSL:1 MANE Select	c.1532+9G>C		intron	N/A	ENSP00000313854.5
	CLPTM1L	ENST00000507807.3	TSL:1	c.1025+9G>C		intron	N/A	ENSP00000423321.1
	CLPTM1L	ENST00000966757.1		c.1736+9G>C		intron	N/A	ENSP00000636816.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome AF: 7.43e-7 AC: 1 AN: 1345936 Hom.: 0 Cov.: 23 AF XY: 0.00000151 AC XY: 1 AN XY: 660318

African (AFR) AF: 0.00 AC: 0 AN: 30068

American (AMR) AF: 0.00 AC: 0 AN: 32546

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24270

East Asian (EAS) AF: 0.00 AC: 0 AN: 34184

South Asian (SAS) AF: 0.0000132 AC: 1 AN: 76012

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 48292

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4016

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1040804

Other (OTH) AF: 0.00 AC: 0 AN: 55744

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.24
PhyloP100		-0.77

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: rs402710; hg19: chr5-1320722;