rs3790506
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020127.3(TUFT1):c.415-273G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 328,736 control chromosomes in the GnomAD database, including 13,260 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 0.26 ( 5576 hom., cov: 32)
Exomes 𝑓: 0.28 ( 7684 hom. )
Consequence
TUFT1
NM_020127.3 intron
NM_020127.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.21
Genes affected
TUFT1 (HGNC:12422): (tuftelin 1) Tuftelin is an acidic protein that is thought to play a role in dental enamel mineralization and is implicated in caries susceptibility. It is also thought to be involved with adaptation to hypoxia, mesenchymal stem cell function, and neurotrophin nerve growth factor mediated neuronal differentiation. [provided by RefSeq, Aug 2014]
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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=-0.94).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUFT1 | NM_020127.3 | c.415-273G>A | intron_variant | ENST00000368849.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUFT1 | ENST00000368849.8 | c.415-273G>A | intron_variant | 1 | NM_020127.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.256 AC: 38825AN: 151794Hom.: 5579 Cov.: 32
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GnomAD4 exome AF: 0.285 AC: 50318AN: 176824Hom.: 7684 Cov.: 0 AF XY: 0.286 AC XY: 26939AN XY: 94048
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GnomAD4 genome ? AF: 0.256 AC: 38829AN: 151912Hom.: 5576 Cov.: 32 AF XY: 0.255 AC XY: 18966AN XY: 74238
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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