rs75791347
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004933.3(CDH15):āc.1750A>Cā(p.Lys584Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 1,535,124 control chromosomes in the GnomAD database, including 143,276 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_004933.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH15 | NM_004933.3 | c.1750A>C | p.Lys584Gln | missense_variant | 11/14 | ENST00000289746.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH15 | ENST00000289746.3 | c.1750A>C | p.Lys584Gln | missense_variant | 11/14 | 1 | NM_004933.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.421 AC: 63857AN: 151728Hom.: 13710 Cov.: 33
GnomAD3 exomes AF: 0.434 AC: 57197AN: 131770Hom.: 12817 AF XY: 0.438 AC XY: 31759AN XY: 72500
GnomAD4 exome AF: 0.430 AC: 594134AN: 1383280Hom.: 129538 Cov.: 55 AF XY: 0.431 AC XY: 294390AN XY: 682780
GnomAD4 genome ? AF: 0.421 AC: 63922AN: 151844Hom.: 13738 Cov.: 33 AF XY: 0.426 AC XY: 31642AN XY: 74210
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 24, 2013 | - - |
Intellectual disability, autosomal dominant 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at