chr20-46174870-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021248.3(CDH22):c.2123G>A(p.Gly708Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000156 in 1,348,194 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_021248.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDH22 | NM_021248.3 | c.2123G>A | p.Gly708Glu | missense_variant | Exon 12 of 12 | ENST00000537909.4 | NP_067071.1 | |
CDH22 | XM_011528994.3 | c.2123G>A | p.Gly708Glu | missense_variant | Exon 12 of 12 | XP_011527296.1 | ||
CDH22 | XM_047440373.1 | c.1883G>A | p.Gly628Glu | missense_variant | Exon 10 of 10 | XP_047296329.1 | ||
CDH22 | XM_024451966.2 | c.1760G>A | p.Gly587Glu | missense_variant | Exon 12 of 12 | XP_024307734.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000795 AC: 12AN: 150922Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000552 AC: 4AN: 72452Hom.: 0 AF XY: 0.0000236 AC XY: 1AN XY: 42316
GnomAD4 exome AF: 0.00000752 AC: 9AN: 1197164Hom.: 0 Cov.: 37 AF XY: 0.00000516 AC XY: 3AN XY: 581586
GnomAD4 genome AF: 0.0000795 AC: 12AN: 151030Hom.: 0 Cov.: 31 AF XY: 0.000122 AC XY: 9AN XY: 73804
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2123G>A (p.G708E) alteration is located in exon 11 (coding exon 11) of the CDH22 gene. This alteration results from a G to A substitution at nucleotide position 2123, causing the glycine (G) at amino acid position 708 to be replaced by a glutamic acid (E). 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