rs149163390
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_001292063.2(OTOG):c.1104-4A>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000441 in 1,547,916 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001292063.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTOG | NM_001292063.2 | c.1104-4A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000399397.6 | |||
OTOG | NM_001277269.2 | c.1140-4A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOG | ENST00000399397.6 | c.1104-4A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001292063.2 | P2 | |||
OTOG | ENST00000399391.7 | c.1140-4A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | A2 | ||||
OTOG | ENST00000498332.5 | n.1010-4A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00237 AC: 360AN: 152184Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000488 AC: 71AN: 145578Hom.: 0 AF XY: 0.000458 AC XY: 36AN XY: 78656
GnomAD4 exome AF: 0.000231 AC: 323AN: 1395614Hom.: 1 Cov.: 31 AF XY: 0.000203 AC XY: 140AN XY: 688506
GnomAD4 genome ? AF: 0.00236 AC: 359AN: 152302Hom.: 1 Cov.: 33 AF XY: 0.00216 AC XY: 161AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 28, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | OTOG: BP4 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 20, 2023 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 24, 2014 | 1140-4A>C in intron 9 of OTOG: This variant is not expected to have clinical sig nificance because it is not located within the conserved splice consensus sequen ce. It has been identified in 1.0% (5/492) of African chromosomes from a broad p opulation by the 1000 Genomes Project (http://www.ncbi.nlm.nih.gov/projects/SNP; dbSNP rs149163390). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at