chr1-151561845-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_020127.3(TUFT1):c.61-246G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00468 in 1,473,388 control chromosomes in the GnomAD database, including 320 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0070 ( 30 hom., cov: 32)
Exomes 𝑓: 0.0044 ( 290 hom. )
Consequence
TUFT1
NM_020127.3 intron
NM_020127.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0400
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 1-151561845-G-A is Benign according to our data. Variant chr1-151561845-G-A is described in ClinVar as [Benign]. Clinvar id is 778237.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0955 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUFT1 | NM_020127.3 | c.61-246G>A | intron_variant | ENST00000368849.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUFT1 | ENST00000368849.8 | c.61-246G>A | intron_variant | 1 | NM_020127.3 | A1 | |||
ENST00000434112.1 | n.516G>A | non_coding_transcript_exon_variant | 2/2 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00701 AC: 1067AN: 152208Hom.: 30 Cov.: 32
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GnomAD3 exomes AF: 0.0246 AC: 3310AN: 134602Hom.: 180 AF XY: 0.0198 AC XY: 1442AN XY: 72688
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GnomAD4 exome AF: 0.00441 AC: 5831AN: 1321062Hom.: 290 Cov.: 32 AF XY: 0.00409 AC XY: 2661AN XY: 650814
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GnomAD4 genome ? AF: 0.00699 AC: 1064AN: 152326Hom.: 30 Cov.: 32 AF XY: 0.00795 AC XY: 592AN XY: 74492
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at