10-133231170-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003577.3(UTF1):c.754C>A(p.Arg252Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000999 in 1,301,508 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003577.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UTF1 | NM_003577.3 | c.754C>A | p.Arg252Ser | missense_variant | 2/2 | ENST00000304477.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UTF1 | ENST00000304477.3 | c.754C>A | p.Arg252Ser | missense_variant | 2/2 | 1 | NM_003577.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000530 AC: 8AN: 151038Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000435 AC: 5AN: 1150470Hom.: 0 Cov.: 35 AF XY: 0.00000718 AC XY: 4AN XY: 557256
GnomAD4 genome AF: 0.0000530 AC: 8AN: 151038Hom.: 0 Cov.: 32 AF XY: 0.0000678 AC XY: 5AN XY: 73746
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 25, 2023 | The c.754C>A (p.R252S) alteration is located in exon 2 (coding exon 2) of the UTF1 gene. This alteration results from a C to A substitution at nucleotide position 754, causing the arginine (R) at amino acid position 252 to be replaced by a serine (S). 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