16-1229648-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024164.6(TPSB2):c.151C>T(p.Arg51Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,604,902 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R51H) has been classified as Likely benign.
Frequency
Consequence
NM_024164.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TPSB2 | NM_024164.6 | c.151C>T | p.Arg51Cys | missense_variant | 3/6 | ENST00000606293.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TPSB2 | ENST00000606293.5 | c.151C>T | p.Arg51Cys | missense_variant | 3/6 | 1 | NM_024164.6 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000203 AC: 3AN: 147946Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.0000203 AC: 5AN: 246246Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133550
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1456956Hom.: 0 Cov.: 90 AF XY: 0.00000552 AC XY: 4AN XY: 724804
GnomAD4 genome AF: 0.0000203 AC: 3AN: 147946Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 72132
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 11, 2022 | The c.151C>T (p.R51C) alteration is located in exon 3 (coding exon 2) of the TPSB2 gene. This alteration results from a C to T substitution at nucleotide position 151, causing the arginine (R) at amino acid position 51 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