X-54091307-C-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_017848.6(FAM120C):c.2427+5G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts 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 Benign (★★).
Frequency
Consequence
NM_017848.6 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAM120C | NM_017848.6 | c.2427+5G>T | splice_region_variant, intron_variant | Intron 11 of 15 | ENST00000375180.7 | NP_060318.4 | ||
FAM120C | NM_001300788.2 | c.2427+5G>T | splice_region_variant, intron_variant | Intron 11 of 13 | NP_001287717.1 | |||
FAM120C | XM_006724589.5 | c.2427+5G>T | splice_region_variant, intron_variant | Intron 11 of 14 | XP_006724652.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FAM120C | ENST00000375180.7 | c.2427+5G>T | splice_region_variant, intron_variant | Intron 11 of 15 | 1 | NM_017848.6 | ENSP00000364324.2 | |||
FAM120C | ENST00000328235.4 | c.2427+5G>T | splice_region_variant, intron_variant | Intron 11 of 13 | 1 | ENSP00000329896.4 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 110456AN: 110941Hom.: 38568 Cov.: 23 AF XY: 0.996 AC XY: 32970AN XY: 33097 FAILED QC
GnomAD3 exomes AF: 0.999 AC: 179200AN: 179444Hom.: 57443 AF XY: 0.999 AC XY: 64113AN XY: 64156
GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 1.00 AC: 1069783AN: 1070307Hom.: 364547 Cov.: 20 AF XY: 1.00 AC XY: 340302AN XY: 340437
GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.996 AC: 110504AN: 110990Hom.: 38563 Cov.: 23 AF XY: 0.996 AC XY: 33028AN XY: 33156
ClinVar
Submissions by phenotype
not provided Benign:2
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This variant was classified as: Benign. The following ACMG criteria were applied in classifying this variant: BS1,BS2. This variant was detected in hemizygous state. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at