rs8192552
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005959.5(MTNR1B):c.71G>A(p.Gly24Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0779 in 1,558,178 control chromosomes in the GnomAD database, including 5,228 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005959.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTNR1B | NM_005959.5 | c.71G>A | p.Gly24Glu | missense_variant | 1/2 | ENST00000257068.3 | |
MTNR1B | XM_011542839.3 | c.71G>A | p.Gly24Glu | missense_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTNR1B | ENST00000257068.3 | c.71G>A | p.Gly24Glu | missense_variant | 1/2 | 1 | NM_005959.5 | P1 | |
MTNR1B | ENST00000528076.1 | c.15G>A | p.Gly5= | synonymous_variant | 1/2 | 3 | |||
MTNR1B | ENST00000532482.1 | c.71G>A | p.Gly24Glu | missense_variant, NMD_transcript_variant | 1/3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0729 AC: 11083AN: 152050Hom.: 495 Cov.: 32
GnomAD3 exomes AF: 0.0678 AC: 13499AN: 199106Hom.: 572 AF XY: 0.0696 AC XY: 7668AN XY: 110164
GnomAD4 exome AF: 0.0785 AC: 110307AN: 1406010Hom.: 4732 Cov.: 32 AF XY: 0.0784 AC XY: 54593AN XY: 696396
GnomAD4 genome AF: 0.0729 AC: 11093AN: 152168Hom.: 496 Cov.: 32 AF XY: 0.0700 AC XY: 5209AN XY: 74394
ClinVar
Submissions by phenotype
MTNR1B-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 24, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at