rs1800885
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_005958.4(MTNR1A):c.160C>T(p.Arg54Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000688 in 1,595,554 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005958.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTNR1A | NM_005958.4 | c.160C>T | p.Arg54Trp | missense_variant | 1/2 | ENST00000307161.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTNR1A | ENST00000307161.5 | c.160C>T | p.Arg54Trp | missense_variant | 1/2 | 1 | NM_005958.4 | P1 | |
MTNR1A | ENST00000703170.1 | c.160C>T | p.Arg54Trp | missense_variant | 1/2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000329 AC: 50AN: 152134Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000532 AC: 116AN: 217858Hom.: 1 AF XY: 0.000534 AC XY: 63AN XY: 117908
GnomAD4 exome AF: 0.000726 AC: 1048AN: 1443302Hom.: 23 Cov.: 31 AF XY: 0.000744 AC XY: 533AN XY: 716366
GnomAD4 genome ? AF: 0.000328 AC: 50AN: 152252Hom.: 1 Cov.: 32 AF XY: 0.000376 AC XY: 28AN XY: 74438
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at