chr19-4910853-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_013282.5(UHRF1):c.7G>T(p.Val3Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000676 in 1,583,434 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 8/10 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_013282.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UHRF1 | NM_001048201.3 | c.-10-23G>T | intron_variant | Intron 1 of 16 | ENST00000650932.1 | NP_001041666.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000493 AC: 75AN: 152176Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000629 AC: 145AN: 230562Hom.: 0 AF XY: 0.000625 AC XY: 78AN XY: 124778
GnomAD4 exome AF: 0.000695 AC: 995AN: 1431258Hom.: 0 Cov.: 29 AF XY: 0.000705 AC XY: 500AN XY: 708974
GnomAD4 genome AF: 0.000493 AC: 75AN: 152176Hom.: 0 Cov.: 31 AF XY: 0.000417 AC XY: 31AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2023 | The c.7G>T (p.V3F) alteration is located in exon 1 (coding exon 1) of the UHRF1 gene. This alteration results from a G to T substitution at nucleotide position 7, causing the valine (V) at amino acid position 3 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | UHRF1: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at