X-54116727-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_017848.6(FAM120C):c.2130G>A(p.Val710Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 1,209,764 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_017848.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAM120C | NM_017848.6 | c.2130G>A | p.Val710Val | synonymous_variant | Exon 10 of 16 | ENST00000375180.7 | NP_060318.4 | |
FAM120C | NM_001300788.2 | c.2130G>A | p.Val710Val | synonymous_variant | Exon 10 of 14 | NP_001287717.1 | ||
FAM120C | XM_006724589.5 | c.2130G>A | p.Val710Val | synonymous_variant | Exon 10 of 15 | XP_006724652.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FAM120C | ENST00000375180.7 | c.2130G>A | p.Val710Val | synonymous_variant | Exon 10 of 16 | 1 | NM_017848.6 | ENSP00000364324.2 | ||
FAM120C | ENST00000328235.4 | c.2130G>A | p.Val710Val | synonymous_variant | Exon 10 of 14 | 1 | ENSP00000329896.4 |
Frequencies
GnomAD3 genomes AF: 0.00000896 AC: 1AN: 111608Hom.: 0 Cov.: 22 AF XY: 0.0000296 AC XY: 1AN XY: 33794
GnomAD4 exome AF: 0.0000137 AC: 15AN: 1098156Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 5AN XY: 363512
GnomAD4 genome AF: 0.00000896 AC: 1AN: 111608Hom.: 0 Cov.: 22 AF XY: 0.0000296 AC XY: 1AN XY: 33794
ClinVar
Submissions by phenotype
not provided Benign:1
FAM120C: BP4, BP7 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at