11-617709-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021924.5(CDHR5):c.2180C>T(p.Ala727Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000363 in 1,458,716 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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 -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDHR5 | NM_021924.5 | c.2180C>T | p.Ala727Val | missense_variant | 15/15 | ENST00000397542.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDHR5 | ENST00000397542.7 | c.2180C>T | p.Ala727Val | missense_variant | 15/15 | 1 | NM_021924.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000275 AC: 2AN: 72854Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 37876
GnomAD4 exome AF: 0.0000344 AC: 45AN: 1306558Hom.: 0 Cov.: 36 AF XY: 0.0000329 AC XY: 21AN XY: 637384
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 23, 2023 | The c.2180C>T (p.A727V) 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 2180, causing the alanine (A) at amino acid position 727 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