22-43128615-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000216115.3(BIK):c.380C>T(p.Pro127Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,610,416 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000216115.3 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BIK | NM_001197.5 | c.380C>T | p.Pro127Leu | missense_variant | 4/5 | ENST00000216115.3 | NP_001188.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BIK | ENST00000216115.3 | c.380C>T | p.Pro127Leu | missense_variant | 4/5 | 1 | NM_001197.5 | ENSP00000216115 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248724Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134468
GnomAD4 exome AF: 0.00000754 AC: 11AN: 1458180Hom.: 0 Cov.: 34 AF XY: 0.00000414 AC XY: 3AN XY: 725116
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.380C>T (p.P127L) alteration is located in exon 4 (coding exon 3) of the BIK gene. This alteration results from a C to T substitution at nucleotide position 380, causing the proline (P) at amino acid position 127 to be replaced by a leucine (L). 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