chr5-24487733-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006727.5(CDH10):c.2297G>A(p.Arg766Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000359 in 1,613,516 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006727.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDH10 | NM_006727.5 | c.2297G>A | p.Arg766Gln | missense_variant | 12/12 | ENST00000264463.8 | NP_006718.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDH10 | ENST00000264463.8 | c.2297G>A | p.Arg766Gln | missense_variant | 12/12 | 1 | NM_006727.5 | ENSP00000264463 | P1 | |
CDH10 | ENST00000510477.5 | c.*849G>A | 3_prime_UTR_variant, NMD_transcript_variant | 11/11 | 1 | ENSP00000425653 | ||||
CDH10 | ENST00000502921.5 | n.1088G>A | non_coding_transcript_exon_variant | 5/5 | 3 | |||||
CDH10 | ENST00000503958.1 | n.820G>A | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000237 AC: 36AN: 151802Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251276Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135806
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461714Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727168
GnomAD4 genome AF: 0.000237 AC: 36AN: 151802Hom.: 0 Cov.: 31 AF XY: 0.000256 AC XY: 19AN XY: 74128
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2021 | The c.2297G>A (p.R766Q) alteration is located in exon 12 (coding exon 11) of the CDH10 gene. This alteration results from a G to A substitution at nucleotide position 2297, causing the arginine (R) at amino acid position 766 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at