15-31483818-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001382637.1(OTUD7A):āc.2278A>Gā(p.Ser760Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.991 in 1,003,664 control chromosomes in the GnomAD database, including 492,514 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_001382637.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OTUD7A | ENST00000307050.6 | c.2278A>G | p.Ser760Gly | missense_variant | 13/13 | 1 | NM_001382637.1 | ENSP00000305926.5 | ||
OTUD7A | ENST00000560598.2 | c.2257A>G | p.Ser753Gly | missense_variant | 14/14 | 5 | ENSP00000453883.2 | |||
OTUD7A | ENST00000678495.1 | c.2257A>G | p.Ser753Gly | missense_variant | 11/11 | ENSP00000503326.1 |
Frequencies
GnomAD3 genomes AF: 0.994 AC: 144370AN: 145172Hom.: 71786 Cov.: 27
GnomAD3 exomes AF: 0.991 AC: 212AN: 214Hom.: 105 AF XY: 0.984 AC XY: 120AN XY: 122
GnomAD4 exome AF: 0.990 AC: 849823AN: 858392Hom.: 420678 Cov.: 47 AF XY: 0.990 AC XY: 394913AN XY: 398918
GnomAD4 genome AF: 0.994 AC: 144470AN: 145272Hom.: 71836 Cov.: 27 AF XY: 0.995 AC XY: 70253AN XY: 70624
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 02, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
OTUD7A-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 12, 2021 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at