11-102324912-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001165.5(BIRC3):c.403C>T(p.Arg135Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000638 in 1,614,154 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001165.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BIRC3 | NM_001165.5 | c.403C>T | p.Arg135Cys | missense_variant | 2/9 | ENST00000263464.9 | NP_001156.1 | |
BIRC3 | NM_182962.3 | c.403C>T | p.Arg135Cys | missense_variant | 3/10 | NP_892007.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BIRC3 | ENST00000263464.9 | c.403C>T | p.Arg135Cys | missense_variant | 2/9 | 1 | NM_001165.5 | ENSP00000263464.4 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251312Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135840
GnomAD4 exome AF: 0.0000670 AC: 98AN: 1461878Hom.: 0 Cov.: 31 AF XY: 0.0000770 AC XY: 56AN XY: 727240
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74440
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 13, 2022 | The c.403C>T (p.R135C) alteration is located in exon 1 (coding exon 1) of the BIRC3 gene. This alteration results from a C to T substitution at nucleotide position 403, causing the arginine (R) at amino acid position 135 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