rs121434539
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4BP6_Very_StrongBS2
The ENST00000289746.3(CDH15):c.178C>T(p.Arg60Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000529 in 1,606,632 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R60H) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000289746.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDH15 | NM_004933.3 | c.178C>T | p.Arg60Cys | missense_variant | 2/14 | ENST00000289746.3 | NP_004924.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDH15 | ENST00000289746.3 | c.178C>T | p.Arg60Cys | missense_variant | 2/14 | 1 | NM_004933.3 | ENSP00000289746 | P1 | |
CDH15 | ENST00000521087.5 | n.243C>T | non_coding_transcript_exon_variant | 2/3 | 5 | |||||
CDH15 | ENST00000524089.1 | n.243C>T | non_coding_transcript_exon_variant | 2/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000118 AC: 29AN: 245476Hom.: 0 AF XY: 0.000143 AC XY: 19AN XY: 132780
GnomAD4 exome AF: 0.0000509 AC: 74AN: 1454434Hom.: 0 Cov.: 32 AF XY: 0.0000609 AC XY: 44AN XY: 722864
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74350
ClinVar
Submissions by phenotype
Intellectual disability, autosomal dominant 3 Pathogenic:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 19, 2022 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 01, 2008 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 18, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at