16-64948660-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000394156.7(CDH11):c.2022A>G(p.Ile674Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,360 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000394156.7 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 |
---|---|---|---|---|---|---|---|
CDH11 | NM_001797.4 | c.1895-561A>G | intron_variant | ENST00000268603.9 | |||
CDH11 | NM_001308392.2 | c.2022A>G | p.Ile674Met | missense_variant | 13/14 | ||
CDH11 | NM_001330576.2 | c.1517-561A>G | intron_variant | ||||
CDH11 | XM_047433486.1 | c.1517-561A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH11 | ENST00000394156.7 | c.2022A>G | p.Ile674Met | missense_variant | 13/14 | 1 | |||
CDH11 | ENST00000268603.9 | c.1895-561A>G | intron_variant | 1 | NM_001797.4 | P1 | |||
CDH11 | ENST00000566827.5 | c.1517-561A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000419 AC: 1AN: 238584Hom.: 0 AF XY: 0.00000763 AC XY: 1AN XY: 131084
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459360Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 725932
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | CDH11: PM2, BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at