chr11-59148935-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_001312909.2(FAM111A):c.63C>T(p.Ile21=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000224 in 1,612,730 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. I21I) has been classified as Uncertain significance.
Frequency
Consequence
NM_001312909.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM111A | NM_001312909.2 | c.63C>T | p.Ile21= | synonymous_variant | 5/6 | ENST00000675163.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM111A | ENST00000675163.1 | c.63C>T | p.Ile21= | synonymous_variant | 5/6 | NM_001312909.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000276 AC: 42AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000482 AC: 121AN: 251086Hom.: 0 AF XY: 0.000494 AC XY: 67AN XY: 135704
GnomAD4 exome AF: 0.000218 AC: 319AN: 1460474Hom.: 0 Cov.: 29 AF XY: 0.000222 AC XY: 161AN XY: 726632
GnomAD4 genome ? AF: 0.000276 AC: 42AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74462
ClinVar
Submissions by phenotype
FAM111A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 18, 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). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at