chr6-170318543-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_032448.3(FAM120B):c.1153C>T(p.Pro385Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000152 in 1,317,468 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 Likely benign (★).
Frequency
Consequence
NM_032448.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM120B | NM_032448.3 | c.1153C>T | p.Pro385Ser | missense_variant | 2/11 | ENST00000476287.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM120B | ENST00000476287.4 | c.1153C>T | p.Pro385Ser | missense_variant | 2/11 | 1 | NM_032448.3 | A2 | |
FAM120B | ENST00000537664.5 | c.1222C>T | p.Pro408Ser | missense_variant | 2/11 | 2 | A2 | ||
FAM120B | ENST00000630384.2 | c.1189C>T | p.Pro397Ser | missense_variant | 2/11 | 2 | A2 | ||
FAM120B | ENST00000625626.1 | c.-90+11701C>T | intron_variant | 2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 6AN: 144616Hom.: 0 Cov.: 32 FAILED QC
GnomAD4 exome AF: 0.00000152 AC: 2AN: 1317468Hom.: 0 Cov.: 37 AF XY: 0.00 AC XY: 0AN XY: 650080
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000415 AC: 6AN: 144616Hom.: 0 Cov.: 32 AF XY: 0.0000285 AC XY: 2AN XY: 70288
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at