1-54139794-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.1076G>A(p.Arg359His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,614,196 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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.1076G>A | p.Arg359His | missense_variant | 4/6 | 5 | NM_001353655.3 | ENSP00000489959.1 | ||
ENSG00000256407 | ENST00000637610.1 | n.*1240G>A | non_coding_transcript_exon_variant | 8/10 | 5 | ENSP00000490901.1 | ||||
ENSG00000256407 | ENST00000637610.1 | n.*1240G>A | 3_prime_UTR_variant | 8/10 | 5 | ENSP00000490901.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251318Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135844
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461878Hom.: 0 Cov.: 34 AF XY: 0.0000220 AC XY: 16AN XY: 727238
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152318Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | The c.1076G>A (p.R359H) 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 1076, causing the arginine (R) at amino acid position 359 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