rs150512674
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBP6
The NM_005422.4(TECTA):c.3103G>A(p.Glu1035Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000564 in 1,614,018 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E1035G) has been classified as Uncertain significance.
Frequency
Consequence
NM_005422.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TECTA | NM_005422.4 | c.3103G>A | p.Glu1035Lys | missense_variant | 11/24 | ENST00000392793.6 | |
TBCEL-TECTA | NM_001378761.1 | c.4060G>A | p.Glu1354Lys | missense_variant | 17/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TECTA | ENST00000392793.6 | c.3103G>A | p.Glu1035Lys | missense_variant | 11/24 | 5 | NM_005422.4 | P4 | |
TECTA | ENST00000264037.2 | c.3103G>A | p.Glu1035Lys | missense_variant | 10/23 | 1 | P4 | ||
TECTA | ENST00000642222.1 | c.3103G>A | p.Glu1035Lys | missense_variant | 11/24 | A1 | |||
TECTA | ENST00000645008.1 | c.412G>A | p.Glu138Lys | missense_variant | 2/15 |
Frequencies
GnomAD3 genomes ? AF: 0.000250 AC: 38AN: 152018Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251336Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135820
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1461882Hom.: 0 Cov.: 32 AF XY: 0.0000275 AC XY: 20AN XY: 727242
GnomAD4 genome ? AF: 0.000250 AC: 38AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.000350 AC XY: 26AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jan 30, 2018 | The p.Glu1035Lys variant in TECTA has not been previously reported in individual s with hearing loss, but has been identified in 0.07% (17/24016) of African chro mosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute .org; dbSNP rs150512674). Although this variant has been seen in the general pop ulation, its frequency is not high enough to rule out a pathogenic role. Computa tional prediction tools and conservation analyses do not provide strong evidence for or against pathogenicity. In summary, the clinical significance of the p.Gl u1035Lys variant is uncertain. ACMG/AMP Criteria applied: none. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 28, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at