chr6-170318087-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032448.3(FAM120B):c.697A>G(p.Ile233Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000044 in 1,614,226 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032448.3 missense
Scores
Clinical Significance
Conservation
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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.697A>G | p.Ile233Val | missense_variant | 2/11 | ENST00000476287.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM120B | ENST00000476287.4 | c.697A>G | p.Ile233Val | missense_variant | 2/11 | 1 | NM_032448.3 | A2 | |
FAM120B | ENST00000537664.5 | c.766A>G | p.Ile256Val | missense_variant | 2/11 | 2 | A2 | ||
FAM120B | ENST00000630384.2 | c.733A>G | p.Ile245Val | missense_variant | 2/11 | 2 | A2 | ||
FAM120B | ENST00000625626.1 | c.-90+11245A>G | intron_variant | 2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 251156Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135834
GnomAD4 exome AF: 0.0000438 AC: 64AN: 1461872Hom.: 0 Cov.: 35 AF XY: 0.0000481 AC XY: 35AN XY: 727228
GnomAD4 genome ? AF: 0.0000459 AC: 7AN: 152354Hom.: 0 Cov.: 33 AF XY: 0.0000268 AC XY: 2AN XY: 74504
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 21, 2022 | The c.697A>G (p.I233V) alteration is located in exon 2 (coding exon 1) of the FAM120B gene. This alteration results from a A to G substitution at nucleotide position 697, causing the isoleucine (I) at amino acid position 233 to be replaced by a valine (V). 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