11-59151775-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001312909.2(FAM111A):c.107G>A(p.Cys36Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00119 in 1,594,248 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001312909.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAM111A | NM_001312909.2 | c.107G>A | p.Cys36Tyr | missense_variant | 6/6 | ENST00000675163.1 | NP_001299838.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FAM111A | ENST00000675163.1 | c.107G>A | p.Cys36Tyr | missense_variant | 6/6 | NM_001312909.2 | ENSP00000501952.1 |
Frequencies
GnomAD3 genomes AF: 0.000618 AC: 94AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00227 AC: 527AN: 231984Hom.: 7 AF XY: 0.00307 AC XY: 385AN XY: 125554
GnomAD4 exome AF: 0.00125 AC: 1805AN: 1441958Hom.: 32 Cov.: 30 AF XY: 0.00175 AC XY: 1258AN XY: 717002
GnomAD4 genome AF: 0.000617 AC: 94AN: 152290Hom.: 0 Cov.: 33 AF XY: 0.000833 AC XY: 62AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 15, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at