rs2289709
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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.*168C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 777,024 control chromosomes in the GnomAD database, including 6,726 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 0.13 ( 1493 hom., cov: 32)
Exomes 𝑓: 0.13 ( 5233 hom. )
Consequence
BMAL2
NM_020183.6 3_prime_UTR
NM_020183.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0730
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=-0.8).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BMAL2 | NM_020183.6 | c.*168C>T | 3_prime_UTR_variant | 17/17 | ENST00000266503.10 | ||
BMAL2-AS1 | NR_109975.1 | n.138+25797G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BMAL2 | ENST00000266503.10 | c.*168C>T | 3_prime_UTR_variant | 17/17 | 1 | NM_020183.6 | P2 | ||
BMAL2 | ENST00000457040.6 | c.*168C>T | 3_prime_UTR_variant | 15/15 | 1 | ||||
BMAL2-AS1 | ENST00000500498.2 | n.129+25797G>A | intron_variant, non_coding_transcript_variant | 1 | |||||
BMAL2 | ENST00000544915.5 | c.*168C>T | 3_prime_UTR_variant | 16/16 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.134 AC: 20395AN: 152062Hom.: 1472 Cov.: 32
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GnomAD4 exome AF: 0.127 AC: 79180AN: 624844Hom.: 5233 Cov.: 9 AF XY: 0.127 AC XY: 39410AN XY: 309152
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GnomAD4 genome ? AF: 0.134 AC: 20452AN: 152180Hom.: 1493 Cov.: 32 AF XY: 0.133 AC XY: 9895AN XY: 74400
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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