chr7-105996344-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_152750.5(CDHR3):c.703C>T(p.Arg235Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000371 in 1,590,310 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R235H) has been classified as Likely benign.
Frequency
Consequence
NM_152750.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDHR3 | NM_152750.5 | c.703C>T | p.Arg235Cys | missense_variant | 6/19 | ENST00000317716.14 | |
CDHR3 | NM_001301161.2 | c.439C>T | p.Arg147Cys | missense_variant | 5/18 | ||
LOC107986833 | XR_001745316.2 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDHR3 | ENST00000317716.14 | c.703C>T | p.Arg235Cys | missense_variant | 6/19 | 1 | NM_152750.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000420 AC: 10AN: 237966Hom.: 0 AF XY: 0.0000619 AC XY: 8AN XY: 129168
GnomAD4 exome AF: 0.0000341 AC: 49AN: 1438112Hom.: 0 Cov.: 29 AF XY: 0.0000295 AC XY: 21AN XY: 710902
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 17, 2023 | The c.703C>T (p.R235C) alteration is located in exon 6 (coding exon 6) of the CDHR3 gene. This alteration results from a C to T substitution at nucleotide position 703, causing the arginine (R) at amino acid position 235 to be replaced by a cysteine (C). 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