1-54140007-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001353655.3(CDCP2):c.863G>A(p.Arg288His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000595 in 1,613,980 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001353655.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDCP2 | ENST00000530059.3 | c.863G>A | p.Arg288His | missense_variant | 4/6 | 5 | NM_001353655.3 | ENSP00000489959.1 | ||
ENSG00000256407 | ENST00000637610.1 | n.*1027G>A | non_coding_transcript_exon_variant | 8/10 | 5 | ENSP00000490901.1 | ||||
ENSG00000256407 | ENST00000637610.1 | n.*1027G>A | 3_prime_UTR_variant | 8/10 | 5 | ENSP00000490901.1 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000443 AC: 11AN: 248310Hom.: 0 AF XY: 0.0000520 AC XY: 7AN XY: 134644
GnomAD4 exome AF: 0.0000547 AC: 80AN: 1461726Hom.: 0 Cov.: 34 AF XY: 0.0000536 AC XY: 39AN XY: 727164
GnomAD4 genome AF: 0.000105 AC: 16AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 02, 2024 | The c.863G>A (p.R288H) alteration is located in exon 4 (coding exon 4) of the CDCP2 gene. This alteration results from a G to A substitution at nucleotide position 863, causing the arginine (R) at amino acid position 288 to be replaced by a histidine (H). 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