16-19536987-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001323572.2(CCP110):c.1318G>T(p.Val440Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000328 in 1,614,082 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001323572.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCP110 | NM_001323572.2 | c.1318G>T | p.Val440Phe | missense_variant | 4/14 | ENST00000694978.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCP110 | ENST00000694978.1 | c.1318G>T | p.Val440Phe | missense_variant | 4/14 | NM_001323572.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000876 AC: 22AN: 251230Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135790
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1461882Hom.: 1 Cov.: 34 AF XY: 0.0000578 AC XY: 42AN XY: 727240
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 11, 2022 | The c.1318G>T (p.V440F) alteration is located in exon 4 (coding exon 3) of the CCP110 gene. This alteration results from a G to T substitution at nucleotide position 1318, causing the valine (V) at amino acid position 440 to be replaced by a phenylalanine (F). 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