NM_152750.5:c.494G>A
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152750.5(CDHR3):c.494G>A(p.Ser165Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000497 in 1,610,034 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152750.5 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00000808 AC: 2AN: 247462 AF XY: 0.00 show subpopulations
GnomAD4 exome AF: 0.00000480 AC: 7AN: 1457840Hom.: 0 Cov.: 30 AF XY: 0.00000690 AC XY: 5AN XY: 725006 show subpopulations
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74350 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.494G>A (p.S165N) alteration is located in exon 4 (coding exon 4) of the CDHR3 gene. This alteration results from a G to A substitution at nucleotide position 494, causing the serine (S) at amino acid position 165 to be replaced by an asparagine (N). 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