11-617406-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_021924.5(CDHR5):c.2483C>T(p.Ala828Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000568 in 1,610,474 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 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. A828T) has been classified as Uncertain significance.
Frequency
Consequence
NM_021924.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDHR5 | NM_021924.5 | c.2483C>T | p.Ala828Val | missense_variant | 15/15 | ENST00000397542.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDHR5 | ENST00000397542.7 | c.2483C>T | p.Ala828Val | missense_variant | 15/15 | 1 | NM_021924.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000394 AC: 60AN: 152116Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000340 AC: 82AN: 241026Hom.: 0 AF XY: 0.000341 AC XY: 45AN XY: 131840
GnomAD4 exome AF: 0.000586 AC: 855AN: 1458240Hom.: 2 Cov.: 32 AF XY: 0.000583 AC XY: 423AN XY: 725440
GnomAD4 genome ? AF: 0.000394 AC: 60AN: 152234Hom.: 0 Cov.: 34 AF XY: 0.000309 AC XY: 23AN XY: 74446
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 03, 2022 | The c.2483C>T (p.A828V) alteration is located in exon 15 (coding exon 15) of the CDHR5 gene. This alteration results from a C to T substitution at nucleotide position 2483, causing the alanine (A) at amino acid position 828 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