chr15-31483895-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001382637.1(OTUD7A):c.2201C>G(p.Pro734Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000238 in 1,008,900 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P734S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001382637.1 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 |
---|---|---|---|---|---|---|---|
OTUD7A | NM_001382637.1 | c.2201C>G | p.Pro734Arg | missense_variant | 13/13 | ENST00000307050.6 | |
OTUD7A | NM_130901.3 | c.2180C>G | p.Pro727Arg | missense_variant | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTUD7A | ENST00000307050.6 | c.2201C>G | p.Pro734Arg | missense_variant | 13/13 | 1 | NM_001382637.1 | P2 | |
OTUD7A | ENST00000560598.2 | c.2180C>G | p.Pro727Arg | missense_variant | 14/14 | 5 | A2 | ||
OTUD7A | ENST00000678495.1 | c.2180C>G | p.Pro727Arg | missense_variant | 11/11 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000548 AC: 8AN: 146062Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.000234 AC: 1AN: 4270Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 2762
GnomAD4 exome AF: 0.0000185 AC: 16AN: 862838Hom.: 0 Cov.: 46 AF XY: 0.00000745 AC XY: 3AN XY: 402868
GnomAD4 genome ? AF: 0.0000548 AC: 8AN: 146062Hom.: 0 Cov.: 29 AF XY: 0.0000563 AC XY: 4AN XY: 71022
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 10, 2023 | The c.2180C>G (p.P727R) alteration is located in exon 11 (coding exon 11) of the OTUD7A gene. This alteration results from a C to G substitution at nucleotide position 2180, causing the proline (P) at amino acid position 727 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