rs4964060
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020183.6(BMAL2):c.484+30A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 1,609,668 control chromosomes in the GnomAD database, including 262,463 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 0.49 ( 20646 hom., cov: 31)
Exomes 𝑓: 0.57 ( 241817 hom. )
Consequence
BMAL2
NM_020183.6 intron
NM_020183.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.907
Genes affected
BMAL2 (HGNC:18984): (basic helix-loop-helix ARNT like 2) This gene encodes a basic helix-loop-helix transcription factor belonging to the PAS (PER, ARNT, SIM) superfamily. The PAS proteins play important roles in adaptation to low atmospheric and cellular oxygen levels, exposure to certain environmental pollutants, and diurnal oscillations in light and temperature. This protein forms a transcriptionally active heterodimer with the circadian CLOCK protein, the structurally related MOP4, and hypoxia-inducible factors, such as HIF1alpha. Consistent with its role as a biologically relevant partner of circadian and hypoxia factors, this protein is coexpressed in regions of the brain such as the thalamus, hypothalamus, and amygdala. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Oct 2011]
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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=-0.94).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BMAL2 | NM_020183.6 | c.484+30A>G | intron_variant | ENST00000266503.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BMAL2 | ENST00000266503.10 | c.484+30A>G | intron_variant | 1 | NM_020183.6 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.491 AC: 74491AN: 151862Hom.: 20633 Cov.: 31
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GnomAD3 exomes AF: 0.562 AC: 140383AN: 249836Hom.: 41879 AF XY: 0.561 AC XY: 75681AN XY: 134984
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GnomAD4 exome AF: 0.569 AC: 829478AN: 1457688Hom.: 241817 Cov.: 32 AF XY: 0.568 AC XY: 411470AN XY: 725022
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GnomAD4 genome ? AF: 0.490 AC: 74527AN: 151980Hom.: 20646 Cov.: 31 AF XY: 0.492 AC XY: 36569AN XY: 74262
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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
RBP_binding_hub_radar
RBP_regulation_power_radar
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