NM_005422.4:c.-1-12T>C
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_005422.4(TECTA):c.-1-12T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0049 in 1,610,968 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_005422.4 intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TECTA | ENST00000392793.6 | c.-1-12T>C | intron_variant | Intron 1 of 23 | 5 | NM_005422.4 | ENSP00000376543.1 | |||
TBCEL-TECTA | ENST00000645041.1 | c.909-12T>C | intron_variant | Intron 6 of 9 | ENSP00000496315.1 |
Frequencies
GnomAD3 genomes AF: 0.00344 AC: 524AN: 152198Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00399 AC: 994AN: 249138Hom.: 7 AF XY: 0.00387 AC XY: 523AN XY: 135094
GnomAD4 exome AF: 0.00505 AC: 7364AN: 1458652Hom.: 32 Cov.: 30 AF XY: 0.00494 AC XY: 3587AN XY: 725920
GnomAD4 genome AF: 0.00344 AC: 524AN: 152316Hom.: 1 Cov.: 32 AF XY: 0.00301 AC XY: 224AN XY: 74474
ClinVar
Submissions by phenotype
not specified Benign:2
-13T>C in Promoter of TECTA: This variant is not expected to have clinical signi ficance because it has been identified in 0.6% (40/7020) of European American ch romosomes from a broad population by the NHLBI Exome Sequencing Project (http:// evs.gs.washingt -
- -
Nonsyndromic Hearing Loss, Dominant Benign:1
- -
not provided Benign:1
- -
Hearing loss, autosomal recessive Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at