2-32357436-A-G
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_016252.4(BIRC6):āc.275A>Gā(p.Lys92Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000161 in 1,549,880 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.000013 ( 0 hom., cov: 32)
Exomes š: 0.000016 ( 0 hom. )
Consequence
BIRC6
NM_016252.4 missense
NM_016252.4 missense
Scores
2
8
6
Clinical Significance
Conservation
PhyloP100: 6.54
Genes affected
BIRC6 (HGNC:13516): (baculoviral IAP repeat containing 6) This gene encodes a protein with a BIR (baculoviral inhibition of apoptosis protein repeat) domain and a UBCc (ubiquitin-conjugating enzyme E2, catalytic) domain. This protein inhibits apoptosis by facilitating the degradation of apoptotic proteins by ubiquitination. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAdExome4 at 23 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BIRC6 | NM_016252.4 | c.275A>G | p.Lys92Arg | missense_variant | 1/74 | ENST00000421745.7 | NP_057336.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BIRC6 | ENST00000421745.7 | c.275A>G | p.Lys92Arg | missense_variant | 1/74 | 1 | NM_016252.4 | ENSP00000393596.2 | ||
BIRC6 | ENST00000700518.1 | c.275A>G | p.Lys92Arg | missense_variant | 1/73 | ENSP00000515025.1 | ||||
BIRC6 | ENST00000700519.1 | c.275A>G | p.Lys92Arg | missense_variant | 1/74 | ENSP00000515026.1 | ||||
BIRC6 | ENST00000648282.1 | c.110A>G | p.Lys37Arg | missense_variant | 1/58 | ENSP00000498175.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152070Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000667 AC: 1AN: 149914Hom.: 0 AF XY: 0.0000125 AC XY: 1AN XY: 80150
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GnomAD4 exome AF: 0.0000165 AC: 23AN: 1397810Hom.: 0 Cov.: 31 AF XY: 0.0000189 AC XY: 13AN XY: 689504
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 152070Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74296
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 27, 2024 | The c.275A>G (p.K92R) alteration is located in exon 1 (coding exon 1) of the BIRC6 gene. This alteration results from a A to G substitution at nucleotide position 275, causing the lysine (K) at amino acid position 92 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Pathogenic
D
MetaRNN
Uncertain
T
MetaSVM
Benign
T
PrimateAI
Pathogenic
D
PROVEAN
Benign
N
REVEL
Uncertain
Sift
Benign
T
Sift4G
Uncertain
D
Vest4
MVP
MPC
ClinPred
D
GERP RS
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at