chr7-76514072-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001347684.2(UPK3B):c.667C>T(p.Arg223Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 1,614,008 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. R223R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001347684.2 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 |
---|---|---|---|---|---|---|---|
UPK3B | NM_001347684.2 | c.667C>T | p.Arg223Cys | missense_variant | 5/6 | ENST00000334348.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UPK3B | ENST00000334348.8 | c.667C>T | p.Arg223Cys | missense_variant | 5/6 | 2 | NM_001347684.2 | P1 | |
UPK3B | ENST00000257632.9 | c.752C>T | p.Ala251Val | missense_variant | 3/4 | 2 | |||
UPK3B | ENST00000394849.1 | c.587C>T | p.Ala196Val | missense_variant | 4/5 | 2 | |||
UPK3B | ENST00000469114.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000500 AC: 76AN: 152094Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000167 AC: 42AN: 251406Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135884
GnomAD4 exome AF: 0.0000636 AC: 93AN: 1461796Hom.: 0 Cov.: 32 AF XY: 0.0000550 AC XY: 40AN XY: 727206
GnomAD4 genome ? AF: 0.000499 AC: 76AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.000443 AC XY: 33AN XY: 74418
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 09, 2024 | The c.752C>T (p.A251V) 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 752, causing the alanine (A) at amino acid position 251 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