2-10441645-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_002539.3(ODC1):c.1105C>T(p.Arg369Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000942 in 1,614,158 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R369H) has been classified as Likely benign.
Frequency
Consequence
NM_002539.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ODC1 | NM_002539.3 | c.1105C>T | p.Arg369Cys | missense_variant | 11/12 | ENST00000234111.9 | |
ODC1 | NM_001287189.2 | c.1105C>T | p.Arg369Cys | missense_variant | 11/12 | ||
ODC1 | NM_001287190.2 | c.1105C>T | p.Arg369Cys | missense_variant | 11/12 | ||
ODC1 | NM_001287188.2 | c.718C>T | p.Arg240Cys | missense_variant | 11/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ODC1 | ENST00000234111.9 | c.1105C>T | p.Arg369Cys | missense_variant | 11/12 | 1 | NM_002539.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000111 AC: 28AN: 251490Hom.: 1 AF XY: 0.000162 AC XY: 22AN XY: 135920
GnomAD4 exome AF: 0.0000978 AC: 143AN: 1461894Hom.: 1 Cov.: 31 AF XY: 0.000118 AC XY: 86AN XY: 727248
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74460
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2022 | ODC1: BP1, BP4, BP5, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at