19-18832400-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_002911.4(UPF1):c.191G>T(p.Gly64Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000466 in 859,114 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002911.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UPF1 | NM_002911.4 | c.191G>T | p.Gly64Val | missense_variant | Exon 1 of 24 | ENST00000262803.10 | NP_002902.2 | |
UPF1 | NM_001297549.2 | c.191G>T | p.Gly64Val | missense_variant | Exon 1 of 24 | NP_001284478.1 | ||
UPF1 | XM_017027105.3 | c.191G>T | p.Gly64Val | missense_variant | Exon 1 of 24 | XP_016882594.1 | ||
UPF1 | XM_017027106.3 | c.191G>T | p.Gly64Val | missense_variant | Exon 1 of 24 | XP_016882595.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000466 AC: 4AN: 859114Hom.: 0 Cov.: 30 AF XY: 0.00000251 AC XY: 1AN XY: 399148
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.191G>T (p.G64V) alteration is located in exon 1 (coding exon 1) of the UPF1 gene. This alteration results from a G to T substitution at nucleotide position 191, causing the glycine (G) at amino acid position 64 to be replaced by a valine (V). 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