chr7-106012871-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152750.5(CDHR3):c.1064C>T(p.Pro355Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000524 in 1,603,242 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P355S) has been classified as Uncertain significance.
Frequency
Consequence
NM_152750.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDHR3 | NM_152750.5 | c.1064C>T | p.Pro355Leu | missense_variant | 9/19 | ENST00000317716.14 | |
CDHR3 | NM_001301161.2 | c.800C>T | p.Pro267Leu | missense_variant | 8/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDHR3 | ENST00000317716.14 | c.1064C>T | p.Pro355Leu | missense_variant | 9/19 | 1 | NM_152750.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000921 AC: 14AN: 152082Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000109 AC: 26AN: 239054Hom.: 0 AF XY: 0.000108 AC XY: 14AN XY: 129618
GnomAD4 exome AF: 0.0000482 AC: 70AN: 1451160Hom.: 0 Cov.: 31 AF XY: 0.0000485 AC XY: 35AN XY: 721472
GnomAD4 genome ? AF: 0.0000921 AC: 14AN: 152082Hom.: 0 Cov.: 32 AF XY: 0.000162 AC XY: 12AN XY: 74284
ClinVar
Submissions by phenotype
Susceptibility to nonsyndromic otitis media Uncertain:1
Uncertain significance, no assertion criteria provided | research | Santos-Cortez Lab, University of Colorado School of Medicine | Feb 01, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at