rs72631819
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000450755.1(TUBB4AP1):n.486G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0101 in 1,131,480 control chromosomes in the GnomAD database, including 59 homozygotes. There are 3,468 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 0.0072 ( 0 hom., 219 hem., cov: 22)
Exomes 𝑓: 0.010 ( 59 hom. 3249 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: 4.09
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BS2
?
High Hemizygotes in GnomAd4 at 219 gene
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.486G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.00726 AC: 811AN: 111781Hom.: 0 Cov.: 22 AF XY: 0.00645 AC XY: 219AN XY: 33935
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GnomAD3 exomes AF: 0.00741 AC: 1360AN: 183437Hom.: 3 AF XY: 0.00803 AC XY: 545AN XY: 67869
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GnomAD4 exome AF: 0.0105 AC: 10666AN: 1019647Hom.: 59 Cov.: 28 AF XY: 0.00999 AC XY: 3249AN XY: 325223
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GnomAD4 genome ? AF: 0.00724 AC: 810AN: 111833Hom.: 0 Cov.: 22 AF XY: 0.00644 AC XY: 219AN XY: 33997
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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