chr16-89179533-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_004933.3(CDH15):c.160G>A(p.Val54Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000382 in 1,610,922 control chromosomes in the GnomAD database, including 5 homozygotes. 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 Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V54L) 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.160G>A | p.Val54Ile | missense_variant | 2/14 | ENST00000289746.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH15 | ENST00000289746.3 | c.160G>A | p.Val54Ile | missense_variant | 2/14 | 1 | NM_004933.3 | P1 | |
CDH15 | ENST00000521087.5 | n.225G>A | non_coding_transcript_exon_variant | 2/3 | 5 | ||||
CDH15 | ENST00000524089.1 | n.225G>A | non_coding_transcript_exon_variant | 2/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000677 AC: 103AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000696 AC: 173AN: 248442Hom.: 4 AF XY: 0.000893 AC XY: 120AN XY: 134424
GnomAD4 exome AF: 0.000352 AC: 513AN: 1458606Hom.: 5 Cov.: 32 AF XY: 0.000474 AC XY: 344AN XY: 725368
GnomAD4 genome AF: 0.000676 AC: 103AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.000846 AC XY: 63AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | CDH15: BS2 - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at