chr16-21678953-C-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBP6_Very_Strong
The NM_144672.4(OTOA):c.120+10C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000493 in 1,613,574 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_144672.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OTOA | ENST00000646100.2 | c.120+10C>G | intron_variant | Intron 3 of 28 | NM_144672.4 | ENSP00000496564.2 | ||||
OTOA | ENST00000388958.8 | c.120+10C>G | intron_variant | Intron 2 of 27 | 1 | ENSP00000373610.3 | ||||
OTOA | ENST00000286149.8 | c.120+10C>G | intron_variant | Intron 2 of 27 | 5 | ENSP00000286149.4 | ||||
OTOA | ENST00000647277.1 | n.120+10C>G | intron_variant | Intron 3 of 28 | ENSP00000495594.1 |
Frequencies
GnomAD3 genomes AF: 0.000427 AC: 65AN: 152114Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000362 AC: 91AN: 251356Hom.: 0 AF XY: 0.000368 AC XY: 50AN XY: 135856
GnomAD4 exome AF: 0.000500 AC: 730AN: 1461460Hom.: 1 Cov.: 33 AF XY: 0.000517 AC XY: 376AN XY: 727048
GnomAD4 genome AF: 0.000427 AC: 65AN: 152114Hom.: 1 Cov.: 32 AF XY: 0.000458 AC XY: 34AN XY: 74270
ClinVar
Submissions by phenotype
not specified Benign:1
120+10C>G in Intron 02 of OTOA: This variant is not expected to have clinical si gnificance because it is not located within the conserved splice consensus seque nce and has been identified in 3/7020 European American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/ EVS). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at