rs11556087
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBA1
The NM_058164.4(OLFM2):c.380C>T(p.Thr127Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 1,613,302 control chromosomes in the GnomAD database, including 36,008 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 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_058164.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OLFM2 | NM_058164.4 | c.380C>T | p.Thr127Met | missense_variant | 4/6 | ENST00000264833.9 | |
OLFM2 | NM_001304347.2 | c.452C>T | p.Thr151Met | missense_variant | 4/6 | ||
OLFM2 | NM_001304348.2 | c.146C>T | p.Thr49Met | missense_variant | 3/5 | ||
OLFM2 | XM_047439713.1 | c.176C>T | p.Thr59Met | missense_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OLFM2 | ENST00000264833.9 | c.380C>T | p.Thr127Met | missense_variant | 4/6 | 1 | NM_058164.4 |
Frequencies
GnomAD3 genomes ? AF: 0.150 AC: 22876AN: 152046Hom.: 2371 Cov.: 32
GnomAD3 exomes AF: 0.153 AC: 38377AN: 250354Hom.: 4068 AF XY: 0.154 AC XY: 20857AN XY: 135334
GnomAD4 exome AF: 0.202 AC: 295778AN: 1461138Hom.: 33639 Cov.: 34 AF XY: 0.199 AC XY: 144379AN XY: 726848
GnomAD4 genome ? AF: 0.150 AC: 22858AN: 152164Hom.: 2369 Cov.: 32 AF XY: 0.142 AC XY: 10589AN XY: 74386
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at