9-93471244-A-G
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP2
The NM_014612.5(FAM120A):c.578A>G(p.Asn193Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Consequence
FAM120A
NM_014612.5 missense
NM_014612.5 missense
Scores
1
10
8
Clinical Significance
Conservation
PhyloP100: 7.31
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP2
Missense variant in gene, where missense usually causes diseases (based on misZ statistic), FAM120A. . Gene score misZ 3.3485 (greater than the threshold 3.09). Trascript score misZ 5.0695 (greater than threshold 3.09). GenCC has associacion of gene with Tourette syndrome.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM120A | NM_014612.5 | c.578A>G | p.Asn193Ser | missense_variant | 2/18 | ENST00000277165.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM120A | ENST00000277165.11 | c.578A>G | p.Asn193Ser | missense_variant | 2/18 | 1 | NM_014612.5 | P3 | |
FAM120A | ENST00000375389.7 | c.578A>G | p.Asn193Ser | missense_variant | 2/9 | 1 | |||
FAM120A | ENST00000698944.1 | c.578A>G | p.Asn193Ser | missense_variant | 2/18 | A1 | |||
FAM120A | ENST00000446420.2 | c.110A>G | p.Asn37Ser | missense_variant | 2/10 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251432Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135884
GnomAD3 exomes
AF:
AC:
1
AN:
251432
Hom.:
AF XY:
AC XY:
1
AN XY:
135884
Gnomad AFR exome
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Gnomad SAS exome
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GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ExAC
AF:
AC:
1
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.578A>G (p.N193S) alteration is located in exon 2 (coding exon 2) of the FAM120A gene. This alteration results from a A to G substitution at nucleotide position 578, causing the asparagine (N) at amino acid position 193 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
T
MetaRNN
Uncertain
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;.
REVEL
Benign
Sift
Uncertain
D;D;.
Sift4G
Uncertain
D;D;D
Polyphen
D;D;.
Vest4
MutPred
Loss of sheet (P = 0.003);Loss of sheet (P = 0.003);.;
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at