chr1-151574969-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020127.3(TUFT1):c.782G>A(p.Arg261Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000351 in 1,422,712 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020127.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUFT1 | NM_020127.3 | c.782G>A | p.Arg261Gln | missense_variant | 9/13 | ENST00000368849.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUFT1 | ENST00000368849.8 | c.782G>A | p.Arg261Gln | missense_variant | 9/13 | 1 | NM_020127.3 | A1 | |
TUFT1 | ENST00000368848.6 | c.707G>A | p.Arg236Gln | missense_variant | 8/12 | 1 | P4 | ||
TUFT1 | ENST00000392712.7 | c.617G>A | p.Arg206Gln | missense_variant | 7/11 | 5 | |||
TUFT1 | ENST00000490156.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 3AN: 187522Hom.: 0 AF XY: 0.0000100 AC XY: 1AN XY: 99538
GnomAD4 exome AF: 0.00000351 AC: 5AN: 1422712Hom.: 0 Cov.: 31 AF XY: 0.00000142 AC XY: 1AN XY: 703616
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 20, 2023 | The c.782G>A (p.R261Q) alteration is located in exon 9 (coding exon 9) of the TUFT1 gene. This alteration results from a G to A substitution at nucleotide position 782, causing the arginine (R) at amino acid position 261 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at