rs1990330
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003213.4(TEAD4):c.1038+188A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,132 control chromosomes in the GnomAD database, including 32,653 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.61 ( 32653 hom., cov: 33)
Consequence
TEAD4
NM_003213.4 intron
NM_003213.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.644
Genes affected
TEAD4 (HGNC:11717): (TEA domain transcription factor 4) This gene product is a member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. Alternatively spliced transcripts encoding distinct isoforms, some of which are translated through the use of a non-AUG (UUG) initiation codon, have been described for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TEAD4 | NM_003213.4 | c.1038+188A>C | intron_variant | ENST00000359864.8 | |||
TEAD4 | NM_201441.3 | c.909+188A>C | intron_variant | ||||
TEAD4 | NM_201443.3 | c.651+188A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEAD4 | ENST00000359864.8 | c.1038+188A>C | intron_variant | 1 | NM_003213.4 | P1 | |||
TEAD4 | ENST00000358409.7 | c.909+188A>C | intron_variant | 1 | |||||
TEAD4 | ENST00000397122.6 | c.651+188A>C | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.607 AC: 92267AN: 152014Hom.: 32645 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.607 AC: 92302AN: 152132Hom.: 32653 Cov.: 33 AF XY: 0.609 AC XY: 45298AN XY: 74372
GnomAD4 genome
?
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74372
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2707
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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