chr10-133231156-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003577.3(UTF1):c.740C>T(p.Pro247Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000266 in 1,245,754 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 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.740C>T | p.Pro247Leu | missense_variant | 2/2 | ENST00000304477.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UTF1 | ENST00000304477.3 | c.740C>T | p.Pro247Leu | missense_variant | 2/2 | 1 | NM_003577.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00124 AC: 186AN: 150494Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000561 AC: 1AN: 1784Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 1232
GnomAD4 exome AF: 0.000133 AC: 146AN: 1095152Hom.: 1 Cov.: 36 AF XY: 0.0000973 AC XY: 51AN XY: 524058
GnomAD4 genome ? AF: 0.00123 AC: 185AN: 150602Hom.: 0 Cov.: 31 AF XY: 0.00118 AC XY: 87AN XY: 73588
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | The c.740C>T (p.P247L) alteration is located in exon 2 (coding exon 2) of the UTF1 gene. This alteration results from a C to T substitution at nucleotide position 740, causing the proline (P) at amino acid position 247 to be replaced by a leucine (L). 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