rs1447351
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000528076.1(MTNR1B):c.*16A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 451,308 control chromosomes in the GnomAD database, including 75,820 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 0.56 ( 23976 hom., cov: 33)
Exomes 𝑓: 0.58 ( 51844 hom. )
Consequence
MTNR1B
ENST00000528076.1 3_prime_UTR
ENST00000528076.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.142
Genes affected
MTNR1B (HGNC:7464): (melatonin receptor 1B) This gene encodes one of two high affinity forms of a receptor for melatonin, the primary hormone secreted by the pineal gland. This gene product is an integral membrane protein that is a G-protein coupled, 7-transmembrane receptor. It is found primarily in the retina and brain although this detection requires RT-PCR. It is thought to participate in light-dependent functions in the retina and may be involved in the neurobiological effects of melatonin. [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=-0.76).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTNR1B | XM_011542839.3 | downstream_gene_variant | |||||
MTNR1B | XM_017017777.2 | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTNR1B | ENST00000528076.1 | c.*16A>G | 3_prime_UTR_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.557 AC: 84639AN: 151924Hom.: 23944 Cov.: 33
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GnomAD3 exomes AF: 0.607 AC: 75236AN: 124000Hom.: 23612 AF XY: 0.604 AC XY: 40966AN XY: 67814
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GnomAD4 exome AF: 0.579 AC: 173359AN: 299268Hom.: 51844 Cov.: 0 AF XY: 0.587 AC XY: 100100AN XY: 170548
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GnomAD4 genome ? AF: 0.557 AC: 84733AN: 152040Hom.: 23976 Cov.: 33 AF XY: 0.565 AC XY: 41996AN XY: 74300
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at