chr6-170318670-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032448.3(FAM120B):āc.1280T>Cā(p.Met427Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000044 in 1,590,318 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_032448.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM120B | NM_032448.3 | c.1280T>C | p.Met427Thr | missense_variant | 2/11 | ENST00000476287.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM120B | ENST00000476287.4 | c.1280T>C | p.Met427Thr | missense_variant | 2/11 | 1 | NM_032448.3 | A2 | |
FAM120B | ENST00000537664.5 | c.1349T>C | p.Met450Thr | missense_variant | 2/11 | 2 | A2 | ||
FAM120B | ENST00000630384.2 | c.1316T>C | p.Met439Thr | missense_variant | 2/11 | 2 | A2 | ||
FAM120B | ENST00000625626.1 | c.-89-11779T>C | intron_variant | 2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151668Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251430Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135888
GnomAD4 exome AF: 0.00000278 AC: 4AN: 1438650Hom.: 0 Cov.: 37 AF XY: 0.00000140 AC XY: 1AN XY: 715198
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151668Hom.: 0 Cov.: 33 AF XY: 0.0000270 AC XY: 2AN XY: 74072
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.1280T>C (p.M427T) alteration is located in exon 2 (coding exon 1) of the FAM120B gene. This alteration results from a T to C substitution at nucleotide position 1280, causing the methionine (M) at amino acid position 427 to be replaced by a threonine (T). 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