11-92969849-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_005959.5(MTNR1B):āc.124G>Cā(p.Ala42Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,609,998 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).
Frequency
Consequence
NM_005959.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTNR1B | NM_005959.5 | c.124G>C | p.Ala42Pro | missense_variant | 1/2 | ENST00000257068.3 | NP_005950.1 | |
MTNR1B | XM_011542839.3 | c.124G>C | p.Ala42Pro | missense_variant | 1/3 | XP_011541141.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTNR1B | ENST00000257068.3 | c.124G>C | p.Ala42Pro | missense_variant | 1/2 | 1 | NM_005959.5 | ENSP00000257068 | P1 | |
MTNR1B | ENST00000528076.1 | c.68G>C | p.Ser23Thr | missense_variant | 1/2 | 3 | ENSP00000433573 | |||
MTNR1B | ENST00000532482.1 | c.124G>C | p.Ala42Pro | missense_variant, NMD_transcript_variant | 1/3 | 5 | ENSP00000436101 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152196Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1457802Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 724952
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
Diabetes mellitus type 2, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Jan 29, 2012 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at