rs141084668
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_004933.3(CDH15):c.598G>A(p.Glu200Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0015 in 1,605,874 control chromosomes in the GnomAD database, including 4 homozygotes. 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 Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E200Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_004933.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH15 | NM_004933.3 | c.598G>A | p.Glu200Lys | missense_variant | 5/14 | ENST00000289746.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH15 | ENST00000289746.3 | c.598G>A | p.Glu200Lys | missense_variant | 5/14 | 1 | NM_004933.3 | P1 | |
CDH15 | ENST00000524089.1 | n.663G>A | non_coding_transcript_exon_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000993 AC: 151AN: 152104Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000788 AC: 185AN: 234764Hom.: 0 AF XY: 0.000699 AC XY: 89AN XY: 127322
GnomAD4 exome AF: 0.00156 AC: 2262AN: 1453652Hom.: 4 Cov.: 32 AF XY: 0.00151 AC XY: 1090AN XY: 722354
GnomAD4 genome ? AF: 0.000992 AC: 151AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.000833 AC XY: 62AN XY: 74440
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 08, 2017 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | CDH15: BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at