chr11-102328092-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001165.5(BIRC3):c.994C>T(p.Arg332Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000516 in 1,609,034 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BIRC3 | NM_001165.5 | c.994C>T | p.Arg332Cys | missense_variant | 4/9 | ENST00000263464.9 | |
BIRC3 | NM_182962.3 | c.994C>T | p.Arg332Cys | missense_variant | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BIRC3 | ENST00000263464.9 | c.994C>T | p.Arg332Cys | missense_variant | 4/9 | 1 | NM_001165.5 | P1 | |
ENST00000673690.1 | n.95+400G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152092Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000183 AC: 45AN: 246314Hom.: 0 AF XY: 0.000135 AC XY: 18AN XY: 133246
GnomAD4 exome AF: 0.0000446 AC: 65AN: 1456942Hom.: 0 Cov.: 30 AF XY: 0.0000442 AC XY: 32AN XY: 724684
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152092Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 10, 2022 | The c.994C>T (p.R332C) 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 994, causing the arginine (R) at amino acid position 332 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