chr19-44987312-A-G
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001294.4(CLPTM1):āc.927A>Gā(p.Pro309=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 1,614,028 control chromosomes in the GnomAD database, including 95,748 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: š 0.39 ( 11929 hom., cov: 35)
Exomes š: 0.33 ( 83819 hom. )
Consequence
CLPTM1
NM_001294.4 synonymous
NM_001294.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -5.33
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP7
Synonymous conserved (PhyloP=-5.33 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLPTM1 | NM_001294.4 | c.927A>G | p.Pro309= | synonymous_variant | 8/14 | ENST00000337392.10 | |
CLPTM1 | NM_001282175.2 | c.885A>G | p.Pro295= | synonymous_variant | 8/14 | ||
CLPTM1 | NM_001282176.2 | c.621A>G | p.Pro207= | synonymous_variant | 8/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLPTM1 | ENST00000337392.10 | c.927A>G | p.Pro309= | synonymous_variant | 8/14 | 1 | NM_001294.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.387 AC: 58857AN: 152056Hom.: 11905 Cov.: 35
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GnomAD3 exomes AF: 0.371 AC: 93177AN: 251422Hom.: 18002 AF XY: 0.361 AC XY: 49084AN XY: 135892
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GnomAD4 exome AF: 0.335 AC: 489197AN: 1461854Hom.: 83819 Cov.: 56 AF XY: 0.333 AC XY: 242378AN XY: 727232
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GnomAD4 genome AF: 0.387 AC: 58934AN: 152174Hom.: 11929 Cov.: 35 AF XY: 0.389 AC XY: 28969AN XY: 74418
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at