chr11-59124180-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_198947.4(FAM111B):c.83A>G(p.Asp28Gly) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000104 in 1,442,888 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198947.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM111B | NM_198947.4 | c.83A>G | p.Asp28Gly | missense_variant, splice_region_variant | 4/4 | ENST00000343597.4 | |
FAM111B | NM_001142703.2 | c.-8A>G | splice_region_variant, 5_prime_UTR_variant | 3/3 | |||
FAM111B | NM_001142704.2 | c.-8A>G | splice_region_variant, 5_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM111B | ENST00000343597.4 | c.83A>G | p.Asp28Gly | missense_variant, splice_region_variant | 4/4 | 1 | NM_198947.4 | P2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000420 AC: 1AN: 238270Hom.: 0 AF XY: 0.00000777 AC XY: 1AN XY: 128716
GnomAD4 exome AF: 0.0000104 AC: 15AN: 1442888Hom.: 1 Cov.: 31 AF XY: 0.0000112 AC XY: 8AN XY: 715954
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 09, 2024 | The c.83A>G (p.D28G) alteration is located in exon 4 (coding exon 2) of the FAM111B gene. This alteration results from a A to G substitution at nucleotide position 83, causing the aspartic acid (D) at amino acid position 28 to be replaced by a glycine (G). 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