11-59109666-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_198947.4(FAM111B):c.41C>T(p.Ala14Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000614 in 1,612,174 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A14S) 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 -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM111B | NM_198947.4 | c.41C>T | p.Ala14Val | missense_variant | 3/4 | ENST00000343597.4 | |
FAM111B | NM_001142703.2 | c.-10+954C>T | intron_variant | ||||
FAM111B | NM_001142704.2 | c.-10+2370C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM111B | ENST00000343597.4 | c.41C>T | p.Ala14Val | missense_variant | 3/4 | 1 | NM_198947.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 250508Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135442
GnomAD4 exome AF: 0.0000610 AC: 89AN: 1460056Hom.: 0 Cov.: 29 AF XY: 0.0000551 AC XY: 40AN XY: 726354
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74308
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | The c.41C>T (p.A14V) alteration is located in exon 3 (coding exon 1) of the FAM111B gene. This alteration results from a C to T substitution at nucleotide position 41, causing the alanine (A) at amino acid position 14 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at