chrX-93709788-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001171109.2(FAM133A):āc.369G>Cā(p.Glu123Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000269 in 1,192,525 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 103 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_001171109.2 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 |
---|---|---|---|---|---|---|---|
FAM133A | NM_001171109.2 | c.369G>C | p.Glu123Asp | missense_variant | 4/4 | ENST00000683942.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM133A | ENST00000683942.1 | c.369G>C | p.Glu123Asp | missense_variant | 4/4 | NM_001171109.2 | P1 | ||
FAM133A | ENST00000322139.4 | c.369G>C | p.Glu123Asp | missense_variant | 3/3 | 4 | P1 | ||
FAM133A | ENST00000332647.5 | c.369G>C | p.Glu123Asp | missense_variant | 4/4 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00142 AC: 157AN: 110893Hom.: 0 Cov.: 22 AF XY: 0.00120 AC XY: 40AN XY: 33251
GnomAD3 exomes AF: 0.000523 AC: 79AN: 151164Hom.: 0 AF XY: 0.000240 AC XY: 11AN XY: 45806
GnomAD4 exome AF: 0.000152 AC: 164AN: 1081587Hom.: 0 Cov.: 31 AF XY: 0.000179 AC XY: 63AN XY: 351653
GnomAD4 genome AF: 0.00142 AC: 157AN: 110938Hom.: 0 Cov.: 22 AF XY: 0.00120 AC XY: 40AN XY: 33306
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 15, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at