chr16-12705010-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_018340.3(CPPED1):c.329G>A(p.Arg110Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00189 in 1,613,622 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018340.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPPED1 | NM_018340.3 | c.329G>A | p.Arg110Gln | missense_variant | 3/4 | ENST00000381774.9 | |
CPPED1 | NM_001099455.2 | c.290-39895G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPPED1 | ENST00000381774.9 | c.329G>A | p.Arg110Gln | missense_variant | 3/4 | 1 | NM_018340.3 | P1 | |
CPPED1 | ENST00000433677.6 | c.290-39895G>A | intron_variant | 1 | |||||
CPPED1 | ENST00000261660.4 | c.290-39990G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00133 AC: 203AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00147 AC: 366AN: 248288Hom.: 0 AF XY: 0.00160 AC XY: 216AN XY: 134762
GnomAD4 exome AF: 0.00194 AC: 2841AN: 1461284Hom.: 2 Cov.: 32 AF XY: 0.00199 AC XY: 1449AN XY: 726852
GnomAD4 genome ? AF: 0.00134 AC: 204AN: 152338Hom.: 0 Cov.: 32 AF XY: 0.00117 AC XY: 87AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 25, 2023 | The c.329G>A (p.R110Q) alteration is located in exon 3 (coding exon 3) of the CPPED1 gene. This alteration results from a G to A substitution at nucleotide position 329, causing the arginine (R) at amino acid position 110 to be replaced by a glutamine (Q). 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