20-2562023-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_080751.3(TMC2):c.554+13C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 1,610,544 control chromosomes in the GnomAD database, including 98,732 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.31 ( 8078 hom., cov: 34)
Exomes 𝑓: 0.35 ( 90654 hom. )
Consequence
TMC2
NM_080751.3 intron
NM_080751.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.965
Genes affected
TMC2 (HGNC:16527): (transmembrane channel like 2) This gene encodes a transmembrane protein that is necesssary for mechanotransduction in cochlear hair cells of the inner ear. Mutations in this gene may underlie hereditary disorders of balance and hearing. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 20-2562023-C-T is Benign according to our data. Variant chr20-2562023-C-T is described in ClinVar as [Benign]. Clinvar id is 1246774.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMC2 | NM_080751.3 | c.554+13C>T | intron_variant | ENST00000358864.2 | |||
TMC2 | XM_005260660.5 | c.629+13C>T | intron_variant | ||||
TMC2 | XR_001754152.2 | n.763+13C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMC2 | ENST00000358864.2 | c.554+13C>T | intron_variant | 1 | NM_080751.3 | P1 | |||
TMC2 | ENST00000644205.1 | n.713+13C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.313 AC: 47667AN: 152126Hom.: 8078 Cov.: 34
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GnomAD3 exomes AF: 0.346 AC: 85111AN: 246262Hom.: 15435 AF XY: 0.349 AC XY: 46600AN XY: 133384
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GnomAD4 exome AF: 0.349 AC: 508805AN: 1458300Hom.: 90654 Cov.: 34 AF XY: 0.350 AC XY: 253530AN XY: 725378
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GnomAD4 genome AF: 0.313 AC: 47680AN: 152244Hom.: 8078 Cov.: 34 AF XY: 0.313 AC XY: 23263AN XY: 74426
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at