19-44961994-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001282176.2(CLPTM1):c.-203C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000144 in 1,457,456 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001282176.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLPTM1 | NM_001294.4 | c.104C>T | p.Pro35Leu | missense_variant | Exon 2 of 14 | ENST00000337392.10 | NP_001285.1 | |
CLPTM1 | NM_001282176.2 | c.-203C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 14 | NP_001269105.1 | |||
CLPTM1 | NM_001282175.2 | c.62C>T | p.Pro21Leu | missense_variant | Exon 2 of 14 | NP_001269104.1 | ||
CLPTM1 | NM_001282176.2 | c.-203C>T | 5_prime_UTR_variant | Exon 2 of 14 | NP_001269105.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000122 AC: 3AN: 245502Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133212
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1457456Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 725236
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.104C>T (p.P35L) alteration is located in exon 2 (coding exon 2) of the CLPTM1 gene. This alteration results from a C to T substitution at nucleotide position 104, causing the proline (P) at amino acid position 35 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at