ENST00000702886.2:n.478A>T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000702886.2(ENSG00000290083):n.478A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 35)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ENSG00000290083
ENST00000702886.2 non_coding_transcript_exon
ENST00000702886.2 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.811
Publications
37 publications found
Genes affected
BMAL1 (HGNC:701): (basic helix-loop-helix ARNT like 1) The protein encoded by this gene is a basic helix-loop-helix protein that forms a heterodimer with CLOCK. This heterodimer binds E-box enhancer elements upstream of Period (PER1, PER2, PER3) and Cryptochrome (CRY1, CRY2) genes and activates transcription of these genes. PER and CRY proteins heterodimerize and repress their own transcription by interacting in a feedback loop with CLOCK/ARNTL complexes. Defects in this gene have been linked to infertility, problems with gluconeogenesis and lipogenesis, and altered sleep patterns. The protein regulates interferon-stimulated gene expression and is an important factor in viral infection, including COVID-19. [provided by RefSeq, Oct 2021]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| BMAL1 | NM_001351804.1 | c.-397T>A | 5_prime_UTR_variant | Exon 1 of 20 | NP_001338733.1 | |||
| BMAL1 | XM_017017738.3 | c.-87T>A | 5_prime_UTR_variant | Exon 1 of 18 | XP_016873227.1 | |||
| BMAL1 | XM_011520105.4 | c.-87T>A | 5_prime_UTR_variant | Exon 1 of 18 | XP_011518407.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000290083 | ENST00000702886.2 | n.478A>T | non_coding_transcript_exon_variant | Exon 1 of 1 | ||||||
| BMAL1 | ENST00000534544.5 | c.-342T>A | 5_prime_UTR_variant | Exon 1 of 5 | 5 | ENSP00000431566.1 | ||||
| BMAL1 | ENST00000529050.5 | c.-216T>A | 5_prime_UTR_variant | Exon 1 of 3 | 4 | ENSP00000434044.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
35
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 10Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 6
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
10
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
6
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
0
AN:
6
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
0
AN:
4
Other (OTH)
AC:
0
AN:
0
GnomAD4 genome
GnomAD4 genome
Cov.:
35
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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