5-134970073-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_178019.3(CATSPER3):c.233G>A(p.Arg78His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,613,950 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_178019.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CATSPER3 | NM_178019.3 | c.233G>A | p.Arg78His | missense_variant | 2/8 | ENST00000282611.8 | NP_821138.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CATSPER3 | ENST00000282611.8 | c.233G>A | p.Arg78His | missense_variant | 2/8 | 1 | NM_178019.3 | ENSP00000282611.6 | ||
PCBD2 | ENST00000504352.1 | n.*152G>A | non_coding_transcript_exon_variant | 5/8 | 5 | ENSP00000426161.1 | ||||
CATSPER3 | ENST00000511235.1 | n.318G>A | non_coding_transcript_exon_variant | 2/3 | 4 | |||||
PCBD2 | ENST00000504352.1 | n.*152G>A | 3_prime_UTR_variant | 5/8 | 5 | ENSP00000426161.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152012Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251430Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135884
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461820Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 727216
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 01, 2024 | The c.233G>A (p.R78H) alteration is located in exon 2 (coding exon 2) of the CATSPER3 gene. This alteration results from a G to A substitution at nucleotide position 233, causing the arginine (R) at amino acid position 78 to be replaced by a histidine (H). 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