chr12-80211955-G-A
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001378609.3(OTOGL):c.126G>A(p.Gly42=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000146 in 1,571,058 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 Benign (★).
Frequency
Genomes: 𝑓 0.00018 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00014 ( 1 hom. )
Consequence
OTOGL
NM_001378609.3 synonymous
NM_001378609.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.490
Genes affected
OTOGL (HGNC:26901): (otogelin like) The protein encoded by this gene belongs to the otogelin family. This gene is expressed in the inner ear of vertebrates with the highest level of expression seen at the embryonic stage and lowest in adult. Knockdown studies in zebrafish suggest that this gene is essential for normal inner ear function. Mutations in this gene are associated with autosomal recessive deafness. [provided by RefSeq, Dec 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
Variant 12-80211955-G-A is Benign according to our data. Variant chr12-80211955-G-A is described in ClinVar as [Benign]. Clinvar id is 2890293.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.49 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTOGL | NM_001378609.3 | c.126G>A | p.Gly42= | synonymous_variant | 4/59 | ENST00000547103.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOGL | ENST00000547103.7 | c.126G>A | p.Gly42= | synonymous_variant | 4/59 | 5 | NM_001378609.3 | P1 | |
OTOGL | ENST00000646859.1 | c.126G>A | p.Gly42= | synonymous_variant | 9/63 | ||||
OTOGL | ENST00000643417.1 | n.786G>A | non_coding_transcript_exon_variant | 7/23 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152136Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000188 AC: 36AN: 191954Hom.: 1 AF XY: 0.000251 AC XY: 26AN XY: 103460
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GnomAD4 exome AF: 0.000142 AC: 202AN: 1418922Hom.: 1 Cov.: 30 AF XY: 0.000146 AC XY: 103AN XY: 703084
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GnomAD4 genome AF: 0.000184 AC: 28AN: 152136Hom.: 1 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74324
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 17, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at