chr11-92981769-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005959.5(MTNR1B):c.546G>T(p.Glu182Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000129 in 1,614,098 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 (★).
Frequency
Consequence
NM_005959.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTNR1B | NM_005959.5 | c.546G>T | p.Glu182Asp | missense_variant | 2/2 | ENST00000257068.3 | NP_005950.1 | |
MTNR1B | XM_011542839.3 | c.546G>T | p.Glu182Asp | missense_variant | 2/3 | XP_011541141.1 | ||
MTNR1B | XM_017017777.2 | c.420G>T | p.Glu140Asp | missense_variant | 2/3 | XP_016873266.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTNR1B | ENST00000257068.3 | c.546G>T | p.Glu182Asp | missense_variant | 2/2 | 1 | NM_005959.5 | ENSP00000257068 | P1 | |
MTNR1B | ENST00000528076.1 | c.166-3038G>T | intron_variant | 3 | ENSP00000433573 | |||||
MTNR1B | ENST00000532482.1 | c.*437G>T | 3_prime_UTR_variant, NMD_transcript_variant | 3/3 | 5 | ENSP00000436101 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000875 AC: 22AN: 251400Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135864
GnomAD4 exome AF: 0.000135 AC: 198AN: 1461892Hom.: 0 Cov.: 31 AF XY: 0.000116 AC XY: 84AN XY: 727248
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | The c.546G>T (p.E182D) alteration is located in exon 2 (coding exon 2) of the MTNR1B gene. This alteration results from a G to T substitution at nucleotide position 546, causing the glutamic acid (E) at amino acid position 182 to be replaced by an aspartic acid (D). 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