chr12-12465759-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_058169.6(BORCS5):c.574C>T(p.Arg192Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,612,758 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 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. R192H) has been classified as Uncertain significance.
Frequency
Consequence
NM_058169.6 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 |
---|---|---|---|---|---|---|---|
BORCS5 | NM_058169.6 | c.574C>T | p.Arg192Cys | missense_variant | 4/4 | ENST00000314565.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BORCS5 | ENST00000314565.9 | c.574C>T | p.Arg192Cys | missense_variant | 4/4 | 1 | NM_058169.6 | P1 | |
BORCS5 | ENST00000298571.6 | c.430C>T | p.Arg144Cys | missense_variant | 3/3 | 1 | |||
BORCS5 | ENST00000542728.5 | c.517C>T | p.Arg173Cys | missense_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000985 AC: 15AN: 152262Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000531 AC: 13AN: 244968Hom.: 0 AF XY: 0.0000525 AC XY: 7AN XY: 133438
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1460496Hom.: 0 Cov.: 34 AF XY: 0.0000220 AC XY: 16AN XY: 726578
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152262Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 11, 2021 | The c.574C>T (p.R192C) alteration is located in exon 4 (coding exon 4) of the BORCS5 gene. This alteration results from a C to T substitution at nucleotide position 574, causing the arginine (R) at amino acid position 192 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