chr16-89179418-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_004933.3(CDH15):āc.45C>Gā(p.Ser15Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,613,494 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. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_004933.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH15 | NM_004933.3 | c.45C>G | p.Ser15Arg | missense_variant, splice_region_variant | 2/14 | ENST00000289746.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH15 | ENST00000289746.3 | c.45C>G | p.Ser15Arg | missense_variant, splice_region_variant | 2/14 | 1 | NM_004933.3 | P1 | |
CDH15 | ENST00000521087.5 | n.110C>G | splice_region_variant, non_coding_transcript_exon_variant | 2/3 | 5 | ||||
CDH15 | ENST00000524089.1 | n.110C>G | splice_region_variant, non_coding_transcript_exon_variant | 2/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000801 AC: 2AN: 249738Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135252
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461260Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 726918
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2022 | The c.45C>G (p.S15R) alteration is located in exon 2 (coding exon 2) of the CDH15 gene. This alteration results from a C to G substitution at nucleotide position 45, causing the serine (S) at amino acid position 15 to be replaced by an arginine (R). 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