rs513349
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001188.4(BAK1):c.532-35T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 1,613,490 control chromosomes in the GnomAD database, including 166,392 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.51 ( 21050 hom., cov: 33)
Exomes 𝑓: 0.43 ( 145342 hom. )
Consequence
BAK1
NM_001188.4 intron
NM_001188.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.842
Genes affected
BAK1 (HGNC:949): (BCL2 antagonist/killer 1) The protein encoded by this gene belongs to the BCL2 protein family. BCL2 family members form oligomers or heterodimers and act as anti- or pro-apoptotic regulators that are involved in a wide variety of cellular activities. This protein localizes to mitochondria, and functions to induce apoptosis. It interacts with and accelerates the opening of the mitochondrial voltage-dependent anion channel, which leads to a loss in membrane potential and the release of cytochrome c. This protein also interacts with the tumor suppressor P53 after exposure to cell stress. [provided by RefSeq, Jul 2008]
GGNBP1 (HGNC:19427): (gametogenetin binding protein 1 (pseudogene)) This gene is the ortholog of the mouse gametogenetin-binding protein 1 gene. In human, the open reading frame is disrupted by a nonsense mutation after 8-aa; consequently, this gene is currently considered to be a unitary pseudogene in human even though it is functional in other mammals. [provided by RefSeq, Aug 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BAK1 | NM_001188.4 | c.532-35T>C | intron_variant | ENST00000374467.4 | |||
BAK1 | XM_011514779.4 | c.532-35T>C | intron_variant | ||||
BAK1 | XM_011514780.2 | c.355-35T>C | intron_variant | ||||
BAK1 | XM_047419196.1 | c.355-35T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BAK1 | ENST00000374467.4 | c.532-35T>C | intron_variant | 1 | NM_001188.4 | P1 | |||
BAK1 | ENST00000442998.6 | c.*90-35T>C | intron_variant | 1 | |||||
GGNBP1 | ENST00000612409.1 | n.249-1409A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.510 AC: 77519AN: 152008Hom.: 20998 Cov.: 33
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GnomAD3 exomes AF: 0.513 AC: 128446AN: 250428Hom.: 35436 AF XY: 0.520 AC XY: 70395AN XY: 135388
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GnomAD4 exome AF: 0.432 AC: 630678AN: 1461364Hom.: 145342 Cov.: 36 AF XY: 0.441 AC XY: 320802AN XY: 726998
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GnomAD4 genome ? AF: 0.510 AC: 77631AN: 152126Hom.: 21050 Cov.: 33 AF XY: 0.520 AC XY: 38694AN XY: 74372
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at