rs72631817
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000450755.1(TUBB4AP1):n.522A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.00746 in 1,092,831 control chromosomes in the GnomAD database, including 351 homozygotes. There are 2,153 hemizygotes in GnomAD. 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 0.036 ( 180 hom., 1108 hem., cov: 22)
Exomes 𝑓: 0.0042 ( 171 hom. 1045 hem. )
Consequence
TUBB4AP1
ENST00000450755.1 non_coding_transcript_exon
ENST00000450755.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.12
Genes affected
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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=-0.64).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBB4AP1 | ENST00000450755.1 | n.522A>G | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.0364 AC: 4062AN: 111664Hom.: 180 Cov.: 22 AF XY: 0.0325 AC XY: 1102AN XY: 33894
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0105 AC: 1935AN: 183483Hom.: 76 AF XY: 0.00695 AC XY: 472AN XY: 67917
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GnomAD4 exome AF: 0.00417 AC: 4091AN: 981113Hom.: 171 Cov.: 27 AF XY: 0.00337 AC XY: 1045AN XY: 310111
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GnomAD4 genome ? AF: 0.0364 AC: 4065AN: 111718Hom.: 180 Cov.: 22 AF XY: 0.0326 AC XY: 1108AN XY: 33958
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at