2-26480789-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_194248.3(OTOF):c.1800G>A(p.Ser600=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,611,348 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000027 ( 0 hom. )
Consequence
OTOF
NM_194248.3 synonymous
NM_194248.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.74
Genes affected
OTOF (HGNC:8515): (otoferlin) Mutations in this gene are a cause of neurosensory nonsyndromic recessive deafness, DFNB9. The short form of the encoded protein has 3 C2 domains, a single carboxy-terminal transmembrane domain found also in the C. elegans spermatogenesis factor FER-1 and human dysferlin, while the long form has 6 C2 domains. The homology suggests that this protein may be involved in vesicle membrane fusion. Several transcript variants encoding multiple isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
Variant 2-26480789-C-T is Benign according to our data. Variant chr2-26480789-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 48179.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-3.74 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTOF | NM_194248.3 | c.1800G>A | p.Ser600= | synonymous_variant | 15/47 | ENST00000272371.7 | |
OTOF | NM_001287489.2 | c.1800G>A | p.Ser600= | synonymous_variant | 15/46 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOF | ENST00000272371.7 | c.1800G>A | p.Ser600= | synonymous_variant | 15/47 | 1 | NM_194248.3 | A1 | |
OTOF | ENST00000403946.7 | c.1800G>A | p.Ser600= | synonymous_variant | 15/46 | 5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152004Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000324 AC: 8AN: 246842Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134288
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GnomAD4 exome AF: 0.0000274 AC: 40AN: 1459344Hom.: 0 Cov.: 33 AF XY: 0.0000262 AC XY: 19AN XY: 725972
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GnomAD4 genome AF: 0.0000395 AC: 6AN: 152004Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74234
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 26, 2012 | Ser600Ser in exon 15 of OTOF: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue and is not located with in the splice consensus sequence. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 22, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at