rs727504781
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP6_Very_Strong
The NM_005422.4(TECTA):c.5273-8del 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 0.0000566 in 1,591,152 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00032 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000029 ( 0 hom. )
Consequence
TECTA
NM_005422.4 splice_region, splice_polypyrimidine_tract, intron
NM_005422.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.07
Genes affected
TECTA (HGNC:11720): (tectorin alpha) The tectorial membrane is an extracellular matrix of the inner ear that contacts the stereocilia bundles of specialized sensory hair cells. Sound induces movement of these hair cells relative to the tectorial membrane, deflects the stereocilia, and leads to fluctuations in hair-cell membrane potential, transducing sound into electrical signals. Alpha-tectorin is one of the major noncollagenous components of the tectorial membrane. Mutations in the TECTA gene have been shown to be responsible for autosomal dominant nonsyndromic hearing impairment and a recessive form of sensorineural pre-lingual non-syndromic deafness. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP6
?
Variant 11-121165264-TC-T is Benign according to our data. Variant chr11-121165264-TC-T is described in ClinVar as [Likely_benign]. Clinvar id is 179309.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TECTA | NM_005422.4 | c.5273-8del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000392793.6 | |||
TBCEL-TECTA | NM_001378761.1 | c.6215-8del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TECTA | ENST00000392793.6 | c.5273-8del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_005422.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000315 AC: 48AN: 152222Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000292 AC: 42AN: 1438812Hom.: 0 Cov.: 31 AF XY: 0.0000196 AC XY: 14AN XY: 713102
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GnomAD4 genome ? AF: 0.000315 AC: 48AN: 152340Hom.: 0 Cov.: 32 AF XY: 0.000349 AC XY: 26AN XY: 74498
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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 | Oct 11, 2013 | 5273-8delC in Intron 15 of TECTA: This variant is not expected to have clinical significance because it is does not diverge from the splice site consensus seque nce and computational tools do not suggest an impact to splicing. In addition, t his variant has been identified in 0.2% (8/4264) of African American chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS/). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 28, 2023 | - - |
Computational scores
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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