7-106004618-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152750.5(CDHR3):c.983G>T(p.Arg328Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000204 in 1,613,994 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R328H) 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDHR3 | NM_152750.5 | c.983G>T | p.Arg328Leu | missense_variant | 8/19 | ENST00000317716.14 | |
CDHR3 | NM_001301161.2 | c.719G>T | p.Arg240Leu | missense_variant | 7/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDHR3 | ENST00000317716.14 | c.983G>T | p.Arg328Leu | missense_variant | 8/19 | 1 | NM_152750.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000986 AC: 15AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249222Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135198
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461700Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727130
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 06, 2023 | The c.983G>T (p.R328L) alteration is located in exon 8 (coding exon 8) of the CDHR3 gene. This alteration results from a G to T substitution at nucleotide position 983, causing the arginine (R) at amino acid position 328 to be replaced by a leucine (L). 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