7-76514074-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_001347684.2(UPK3B):c.669C>T(p.Arg223=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,894 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001347684.2 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UPK3B | NM_001347684.2 | c.669C>T | p.Arg223= | splice_region_variant, synonymous_variant | 5/6 | ENST00000334348.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UPK3B | ENST00000334348.8 | c.669C>T | p.Arg223= | splice_region_variant, synonymous_variant | 5/6 | 2 | NM_001347684.2 | P1 | |
UPK3B | ENST00000257632.9 | c.754C>T | p.Leu252Phe | missense_variant, splice_region_variant | 3/4 | 2 | |||
UPK3B | ENST00000394849.1 | c.589C>T | p.Leu197Phe | missense_variant, splice_region_variant | 4/5 | 2 | |||
UPK3B | ENST00000469114.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152086Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461808Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727222
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152086Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74278
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 06, 2023 | The c.754C>T (p.L252F) alteration is located in exon 3 (coding exon 3) of the UPK3B gene. This alteration results from a C to T substitution at nucleotide position 754, causing the leucine (L) at amino acid position 252 to be replaced by a phenylalanine (F). 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