rs533096070
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_138501.6(TECR):c.606+7A>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000799 in 1,613,834 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138501.6 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TECR | NM_138501.6 | c.606+7A>C | splice_region_variant, intron_variant | ENST00000215567.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TECR | ENST00000215567.10 | c.606+7A>C | splice_region_variant, intron_variant | 1 | NM_138501.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 151992Hom.: 1 Cov.: 30
GnomAD3 exomes AF: 0.000207 AC: 52AN: 251050Hom.: 0 AF XY: 0.000243 AC XY: 33AN XY: 135824
GnomAD4 exome AF: 0.0000828 AC: 121AN: 1461724Hom.: 1 Cov.: 34 AF XY: 0.000116 AC XY: 84AN XY: 727162
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152110Hom.: 1 Cov.: 30 AF XY: 0.0000672 AC XY: 5AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 21, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at