19-48303782-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001364171.2(ODAD1):āc.856G>Cā(p.Gly286Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,454,500 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin ClinVar.
Frequency
Consequence
NM_001364171.2 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
ODAD1 | NM_001364171.2 | c.856G>C | p.Gly286Arg | missense_variant, splice_region_variant | 10/16 | ENST00000674294.1 | |
ODAD1 | NM_144577.4 | c.745G>C | p.Gly249Arg | missense_variant, splice_region_variant | 8/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ODAD1 | ENST00000674294.1 | c.856G>C | p.Gly286Arg | missense_variant, splice_region_variant | 10/16 | NM_001364171.2 | P2 | ||
ODAD1 | ENST00000315396.7 | c.745G>C | p.Gly249Arg | missense_variant, splice_region_variant | 8/14 | 1 | A2 | ||
ODAD1 | ENST00000474199.6 | c.856G>C | p.Gly286Arg | missense_variant, splice_region_variant | 10/15 | 2 | A2 | ||
ODAD1 | ENST00000674207.1 | c.*564G>C | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 8/13 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000823 AC: 2AN: 243150Hom.: 0 AF XY: 0.00000762 AC XY: 1AN XY: 131182
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1454500Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 723192
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at