chr11-59124377-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_198947.4(FAM111B):c.280C>T(p.Arg94Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000285 in 1,613,588 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R94G) has been classified as Uncertain significance.
Frequency
Consequence
NM_198947.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM111B | NM_198947.4 | c.280C>T | p.Arg94Cys | missense_variant | 4/4 | ENST00000343597.4 | |
FAM111B | NM_001142703.2 | c.190C>T | p.Arg64Cys | missense_variant | 3/3 | ||
FAM111B | NM_001142704.2 | c.190C>T | p.Arg64Cys | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM111B | ENST00000343597.4 | c.280C>T | p.Arg94Cys | missense_variant | 4/4 | 1 | NM_198947.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000132 AC: 20AN: 152004Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000626 AC: 157AN: 250842Hom.: 0 AF XY: 0.000900 AC XY: 122AN XY: 135570
GnomAD4 exome AF: 0.000301 AC: 440AN: 1461466Hom.: 1 Cov.: 32 AF XY: 0.000435 AC XY: 316AN XY: 727022
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152122Hom.: 1 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74374
ClinVar
Submissions by phenotype
FAM111B-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 10, 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