chr11-12862299-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_021961.6(TEAD1):c.252G>A(p.Thr84=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000601 in 1,613,930 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T84T) has been classified as Likely benign.
Frequency
Consequence
NM_021961.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TEAD1 | NM_021961.6 | c.252G>A | p.Thr84= | synonymous_variant | 4/13 | ENST00000527636.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEAD1 | ENST00000527636.7 | c.252G>A | p.Thr84= | synonymous_variant | 4/13 | 1 | NM_021961.6 | ||
TEAD1 | ENST00000334310.10 | c.207G>A | p.Thr69= | synonymous_variant | 3/12 | 1 | P1 | ||
TEAD1 | ENST00000525312.1 | n.265G>A | non_coding_transcript_exon_variant | 2/3 | 1 | ||||
TEAD1 | ENST00000527575.6 | c.252G>A | p.Thr84= | synonymous_variant | 3/11 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000921 AC: 14AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251220Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135756
GnomAD4 exome AF: 0.0000561 AC: 82AN: 1461724Hom.: 0 Cov.: 30 AF XY: 0.0000564 AC XY: 41AN XY: 727172
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74406
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at