chr6-170318501-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_032448.3(FAM120B):c.1111T>C(p.Ser371Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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
Genomes: 𝑓 0.00015 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
FAM120B
NM_032448.3 missense
NM_032448.3 missense
Scores
14
Clinical Significance
Conservation
PhyloP100: -0.285
Genes affected
FAM120B (HGNC:21109): (family with sequence similarity 120 member B) Predicted to be involved in fat cell differentiation and peroxisome proliferator activated receptor signaling pathway. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.021270841).
BP6
?
Variant 6-170318501-T-C is Benign according to our data. Variant chr6-170318501-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2608953.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM120B | NM_032448.3 | c.1111T>C | p.Ser371Pro | missense_variant | 2/11 | ENST00000476287.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM120B | ENST00000476287.4 | c.1111T>C | p.Ser371Pro | missense_variant | 2/11 | 1 | NM_032448.3 | A2 | |
FAM120B | ENST00000537664.5 | c.1180T>C | p.Ser394Pro | missense_variant | 2/11 | 2 | A2 | ||
FAM120B | ENST00000630384.2 | c.1147T>C | p.Ser383Pro | missense_variant | 2/11 | 2 | A2 | ||
FAM120B | ENST00000625626.1 | c.-90+11659T>C | intron_variant | 2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 21AN: 138252Hom.: 0 Cov.: 32 FAILED QC
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FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1430022Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 710698
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.000152 AC: 21AN: 138380Hom.: 0 Cov.: 32 AF XY: 0.000163 AC XY: 11AN XY: 67584
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 30, 2023 | 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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N
PrimateAI
Benign
T
Sift4G
Benign
T;T;T
Polyphen
0.0
.;.;B
Vest4
MutPred
0.12
.;.;Loss of phosphorylation at S371 (P = 0.0085);
MVP
MPC
0.22
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at