11-92981680-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005959.5(MTNR1B):c.457C>T(p.Arg153Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000421 in 1,614,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R153L) has been classified as Uncertain significance.
Frequency
Consequence
NM_005959.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTNR1B | NM_005959.5 | c.457C>T | p.Arg153Trp | missense_variant | Exon 2 of 2 | ENST00000257068.3 | NP_005950.1 | |
MTNR1B | XM_011542839.3 | c.457C>T | p.Arg153Trp | missense_variant | Exon 2 of 3 | XP_011541141.1 | ||
MTNR1B | XM_017017777.2 | c.331C>T | p.Arg111Trp | missense_variant | Exon 2 of 3 | XP_016873266.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTNR1B | ENST00000257068.3 | c.457C>T | p.Arg153Trp | missense_variant | Exon 2 of 2 | 1 | NM_005959.5 | ENSP00000257068.2 | ||
MTNR1B | ENST00000528076.1 | c.165-3127C>T | intron_variant | Intron 1 of 1 | 3 | ENSP00000433573.1 | ||||
MTNR1B | ENST00000532482.1 | n.*348C>T | non_coding_transcript_exon_variant | Exon 3 of 3 | 5 | ENSP00000436101.1 | ||||
MTNR1B | ENST00000532482.1 | n.*348C>T | 3_prime_UTR_variant | Exon 3 of 3 | 5 | ENSP00000436101.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251420Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135878
GnomAD4 exome AF: 0.0000431 AC: 63AN: 1461894Hom.: 0 Cov.: 31 AF XY: 0.0000481 AC XY: 35AN XY: 727248
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.457C>T (p.R153W) alteration is located in exon 2 (coding exon 2) of the MTNR1B gene. This alteration results from a C to T substitution at nucleotide position 457, causing the arginine (R) at amino acid position 153 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at