22-43129222-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001197.5(BIK):c.400G>A(p.Glu134Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000517 in 1,604,712 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_001197.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BIK | NM_001197.5 | c.400G>A | p.Glu134Lys | missense_variant | Exon 5 of 5 | ENST00000216115.3 | NP_001188.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152042Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000129 AC: 31AN: 240912Hom.: 0 AF XY: 0.000114 AC XY: 15AN XY: 131832
GnomAD4 exome AF: 0.0000441 AC: 64AN: 1452552Hom.: 0 Cov.: 35 AF XY: 0.0000553 AC XY: 40AN XY: 722952
GnomAD4 genome AF: 0.000125 AC: 19AN: 152160Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74398
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.400G>A (p.E134K) alteration is located in exon 5 (coding exon 4) of the BIK gene. This alteration results from a G to A substitution at nucleotide position 400, causing the glutamic acid (E) at amino acid position 134 to be replaced by a lysine (K). 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