chr11-92981816-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_005959.5(MTNR1B):c.593C>A(p.Thr198Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000228 in 1,614,216 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005959.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTNR1B | NM_005959.5 | c.593C>A | p.Thr198Asn | missense_variant | 2/2 | ENST00000257068.3 | |
MTNR1B | XM_011542839.3 | c.593C>A | p.Thr198Asn | missense_variant | 2/3 | ||
MTNR1B | XM_017017777.2 | c.467C>A | p.Thr156Asn | missense_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTNR1B | ENST00000257068.3 | c.593C>A | p.Thr198Asn | missense_variant | 2/2 | 1 | NM_005959.5 | P1 | |
MTNR1B | ENST00000528076.1 | c.166-2991C>A | intron_variant | 3 | |||||
MTNR1B | ENST00000532482.1 | c.*484C>A | 3_prime_UTR_variant, NMD_transcript_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152206Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000414 AC: 104AN: 251452Hom.: 0 AF XY: 0.000567 AC XY: 77AN XY: 135900
GnomAD4 exome AF: 0.000241 AC: 352AN: 1461892Hom.: 5 Cov.: 31 AF XY: 0.000378 AC XY: 275AN XY: 727248
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152324Hom.: 1 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74472
ClinVar
Submissions by phenotype
MTNR1B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 14, 2020 | This variant is classified as likely 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