1-54139756-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001353655.3(CDCP2):c.1114G>A(p.Gly372Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000376 in 1,614,228 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts 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 Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDCP2 | ENST00000530059.3 | c.1114G>A | p.Gly372Arg | missense_variant | Exon 4 of 6 | 5 | NM_001353655.3 | ENSP00000489959.1 | ||
ENSG00000256407 | ENST00000637610.1 | n.*1278G>A | non_coding_transcript_exon_variant | Exon 8 of 10 | 5 | ENSP00000490901.1 | ||||
ENSG00000256407 | ENST00000637610.1 | n.*1278G>A | 3_prime_UTR_variant | Exon 8 of 10 | 5 | ENSP00000490901.1 |
Frequencies
GnomAD3 genomes AF: 0.000499 AC: 76AN: 152222Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000362 AC: 91AN: 251292Hom.: 0 AF XY: 0.000302 AC XY: 41AN XY: 135852
GnomAD4 exome AF: 0.000363 AC: 531AN: 1461888Hom.: 0 Cov.: 34 AF XY: 0.000369 AC XY: 268AN XY: 727246
GnomAD4 genome AF: 0.000499 AC: 76AN: 152340Hom.: 2 Cov.: 32 AF XY: 0.000430 AC XY: 32AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1114G>A (p.G372R) 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 1114, causing the glycine (G) at amino acid position 372 to be replaced by an arginine (R). 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