Genetic Variant FAM120AOS:p.Leu156Phe (chr9-93452242-C-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_198841.4(FAM120AOS):c.468G>C(p.Leu156Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

FAM120AOS
NM_198841.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.24

Publications

0 publications found

Variant links:

Genes affected

FAM120AOS (HGNC:23389): (family with sequence similarity 120 member A opposite strand) Differences in the expression level of this gene are associated with the survival rate of those with glioma. [provided by RefSeq, May 2017]

FAM120AOS links:

FAM120A (HGNC:13247): (family with sequence similarity 120 member A) Enables RNA binding activity. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

FAM120A Gene-Disease associations (from GenCC):

Tourette syndrome
Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

FAM120A links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.17264357).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198841.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FAM120AOS	NM_198841.4	MANE Select	c.468G>C	p.Leu156Phe	missense	Exon 1 of 3	NP_942138.2	Q5T036
FAM120A	NM_014612.5	MANE Select	c.327C>G	p.Val109Val	synonymous	Exon 1 of 18	NP_055427.2
FAM120A	NM_001439102.1		c.327C>G	p.Val109Val	synonymous	Exon 1 of 19	NP_001426031.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FAM120AOS	ENST00000375412.11	TSL:1 MANE Select	c.468G>C	p.Leu156Phe	missense	Exon 1 of 3	ENSP00000364561.5	Q5T036
FAM120A	ENST00000277165.11	TSL:1 MANE Select	c.327C>G	p.Val109Val	synonymous	Exon 1 of 18	ENSP00000277165.5	Q9NZB2-1
FAM120A	ENST00000375389.7	TSL:1	c.327C>G	p.Val109Val	synonymous	Exon 1 of 9	ENSP00000364538.3	Q9NZB2-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1459160

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

725838

African (AFR)

AF:

0.00

AC:

AN:

33458

American (AMR)

AF:

0.00

AC:

AN:

44554

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26082

East Asian (EAS)

AF:

0.00

AC:

AN:

39638

South Asian (SAS)

AF:

0.00

AC:

AN:

86054

European-Finnish (FIN)

AF:

0.00

AC:

AN:

51858

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5758

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1111480

Other (OTH)

AF:

0.00

AC:

AN:

60278

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.72

BayesDel_addAF

Uncertain

0.036

BayesDel_noAF

Benign

-0.19

CADD

Uncertain

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.023

Eigen

Benign

-0.13

Eigen_PC

Benign

-0.10

FATHMM_MKL

Benign

0.43

LIST_S2

Benign

0.43

M_CAP

Pathogenic

0.48

MetaRNN

Benign

0.17

MetaSVM

Benign

-0.95

MutationAssessor

Benign

0.0

PhyloP100

1.2

PrimateAI

Pathogenic

0.90

PROVEAN

Benign

-2.3

REVEL

Benign

0.16

Sift

Pathogenic

0.0

Sift4G

Benign

0.36

Polyphen

0.94

Vest4

0.057

MutPred

0.18

Gain of sheet (P = 0.1208)

MVP

0.10

MPC

0.85

ClinPred

0.49

GERP RS

1.8

PromoterAI

0.0062

Neutral

(source)

Varity_R

0.44

gMVP

0.029

Mutation Taster

=90/10

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over