rs1946295
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_181486.4(TBX5):c.982+1609T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.697 in 151,980 control chromosomes in the GnomAD database, including 37,395 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 0.70 ( 37395 hom., cov: 31)
Consequence
TBX5
NM_181486.4 intron
NM_181486.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.619
Genes affected
TBX5 (HGNC:11604): (T-box transcription factor 5) This gene is a member of a phylogenetically conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of developmental processes. This gene is closely linked to related family member T-box 3 (ulnar mammary syndrome) on human chromosome 12. The encoded protein may play a role in heart development and specification of limb identity. Mutations in this gene have been associated with Holt-Oram syndrome, a developmental disorder affecting the heart and upper limbs. Several transcript variants encoding different isoforms 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=-0.95).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX5 | NM_181486.4 | c.982+1609T>C | intron_variant | ENST00000405440.7 | |||
TBX5 | NM_000192.3 | c.982+1609T>C | intron_variant | ||||
TBX5 | NM_080717.4 | c.832+1609T>C | intron_variant | ||||
TBX5 | XM_017019912.2 | c.1030+1609T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX5 | ENST00000405440.7 | c.982+1609T>C | intron_variant | 1 | NM_181486.4 | P1 | |||
TBX5 | ENST00000310346.8 | c.982+1609T>C | intron_variant | 1 | P1 | ||||
TBX5 | ENST00000349716.9 | c.832+1609T>C | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.697 AC: 105905AN: 151862Hom.: 37371 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.697 AC: 105972AN: 151980Hom.: 37395 Cov.: 31 AF XY: 0.692 AC XY: 51439AN XY: 74290
GnomAD4 genome
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2175
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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