rs210134
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000612409.1(GGNBP1):n.248+1621A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,730 control chromosomes in the GnomAD database, including 39,825 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 0.72 ( 39648 hom., cov: 31)
Exomes 𝑓: 0.73 ( 177 hom. )
Consequence
GGNBP1
ENST00000612409.1 intron
ENST00000612409.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.774
Genes affected
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]
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]
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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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BAK1 | NM_001188.4 | c.*1371T>C | downstream_gene_variant | ENST00000374467.4 | NP_001179.1 | |||
BAK1 | XM_011514779.4 | c.*1371T>C | downstream_gene_variant | XP_011513081.1 | ||||
BAK1 | XM_011514780.2 | c.*1371T>C | downstream_gene_variant | XP_011513082.1 | ||||
BAK1 | XM_047419196.1 | c.*1371T>C | downstream_gene_variant | XP_047275152.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GGNBP1 | ENST00000612409.1 | n.248+1621A>G | intron_variant | Intron 3 of 5 | 5 | |||||
BAK1 | ENST00000374467.4 | c.*1371T>C | downstream_gene_variant | 1 | NM_001188.4 | ENSP00000363591.3 | ||||
BAK1 | ENST00000442998.6 | c.*1565T>C | downstream_gene_variant | 1 | ENSP00000391258.2 |
Frequencies
GnomAD3 genomes AF: 0.721 AC: 109613AN: 151956Hom.: 39610 Cov.: 31
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GnomAD4 exome AF: 0.732 AC: 480AN: 656Hom.: 177 AF XY: 0.760 AC XY: 254AN XY: 334
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GnomAD4 genome AF: 0.721 AC: 109704AN: 152074Hom.: 39648 Cov.: 31 AF XY: 0.725 AC XY: 53906AN XY: 74344
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at