rs6142884
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001794.5(CDH4):c.1874A>G(p.Lys625Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 1,610,020 control chromosomes in the GnomAD database, including 234,382 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001794.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH4 | NM_001794.5 | c.1874A>G | p.Lys625Arg | missense_variant | 12/16 | ENST00000614565.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH4 | ENST00000614565.5 | c.1874A>G | p.Lys625Arg | missense_variant | 12/16 | 1 | NM_001794.5 | P1 | |
CDH4 | ENST00000543233.2 | c.1652A>G | p.Lys551Arg | missense_variant | 11/15 | 2 | |||
CDH4 | ENST00000611855.4 | c.1592A>G | p.Lys531Arg | missense_variant | 11/15 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.491 AC: 74575AN: 152030Hom.: 19594 Cov.: 34
GnomAD3 exomes AF: 0.576 AC: 142748AN: 247634Hom.: 43408 AF XY: 0.577 AC XY: 77482AN XY: 134276
GnomAD4 exome AF: 0.536 AC: 781247AN: 1457872Hom.: 214767 Cov.: 56 AF XY: 0.540 AC XY: 391855AN XY: 725414
GnomAD4 genome ? AF: 0.490 AC: 74618AN: 152148Hom.: 19615 Cov.: 34 AF XY: 0.500 AC XY: 37182AN XY: 74396
ClinVar
Submissions by phenotype
CDH4-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at