chr5-19473351-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004934.5(CDH18):c.2248A>G(p.Ile750Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000415 in 1,613,824 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004934.5 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 | UniProt |
---|---|---|---|---|---|---|---|
CDH18 | NM_004934.5 | c.2248A>G | p.Ile750Val | missense_variant | 13/13 | ENST00000382275.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH18 | ENST00000382275.6 | c.2248A>G | p.Ile750Val | missense_variant | 13/13 | 1 | NM_004934.5 | P1 | |
CDH18 | ENST00000274170.8 | c.2248A>G | p.Ile750Val | missense_variant | 11/11 | 1 | P1 | ||
CDH18 | ENST00000507958.5 | c.2248A>G | p.Ile750Val | missense_variant | 15/15 | 2 | P1 | ||
CDH18 | ENST00000510297.1 | n.499A>G | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000210 AC: 32AN: 152134Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250946Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135606
GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461690Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 16AN XY: 727158
GnomAD4 genome ? AF: 0.000210 AC: 32AN: 152134Hom.: 0 Cov.: 31 AF XY: 0.000215 AC XY: 16AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 10, 2022 | The c.2248A>G (p.I750V) alteration is located in exon 13 (coding exon 11) of the CDH18 gene. This alteration results from a A to G substitution at nucleotide position 2248, causing the isoleucine (I) at amino acid position 750 to be replaced by a valine (V). 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