7-76511879-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001347684.2(UPK3B):c.458A>G(p.Tyr153Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00011 in 1,392,260 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UPK3B | NM_001347684.2 | c.458A>G | p.Tyr153Cys | missense_variant | Exon 3 of 6 | ENST00000334348.8 | NP_001334613.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000499 AC: 75AN: 150424Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.000295 AC: 14AN: 47524Hom.: 0 AF XY: 0.000292 AC XY: 7AN XY: 23984
GnomAD4 exome AF: 0.0000636 AC: 79AN: 1241714Hom.: 0 Cov.: 22 AF XY: 0.0000432 AC XY: 26AN XY: 602336
GnomAD4 genome AF: 0.000492 AC: 74AN: 150546Hom.: 0 Cov.: 28 AF XY: 0.000436 AC XY: 32AN XY: 73458
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.623A>G (p.Y208C) alteration is located in exon 2 (coding exon 2) of the UPK3B gene. This alteration results from a A to G substitution at nucleotide position 623, causing the tyrosine (Y) at amino acid position 208 to be replaced by a cysteine (C). 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