9-93452218-G-C

Variant names:

• chr9-93452218-G-C
• rs1416988256
• NM_014612.5:c.303G>C

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_014612.5(FAM120A):​c.303G>C​(p.Glu101Asp) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: FAM120A NM_014612.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.07
• Publications: 0 publications found

Genes affected

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]

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.30071932).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014612.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM120A	NM_014612.5	MANE Select	c.303G>C	p.Glu101Asp	missense	Exon 1 of 18	NP_055427.2
	FAM120AOS	NM_198841.4	MANE Select	c.492C>G	p.Phe164Leu	missense	Exon 1 of 3	NP_942138.2	Q5T036
	FAM120A	NM_001439102.1		c.303G>C	p.Glu101Asp	missense	Exon 1 of 19	NP_001426031.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM120A	ENST00000277165.11	TSL:1 MANE Select	c.303G>C	p.Glu101Asp	missense	Exon 1 of 18	ENSP00000277165.5	Q9NZB2-1
	FAM120AOS	ENST00000375412.11	TSL:1 MANE Select	c.492C>G	p.Phe164Leu	missense	Exon 1 of 3	ENSP00000364561.5	Q5T036
	FAM120A	ENST00000375389.7	TSL:1	c.303G>C	p.Glu101Asp	missense	Exon 1 of 9	ENSP00000364538.3	Q9NZB2-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.33
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.41
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Benign	0.065	T
Eigen	Uncertain	0.22
Eigen_PC	Uncertain	0.27
FATHMM_MKL	Uncertain	0.82	D
LIST_S2	Uncertain	0.94	D
M_CAP	Pathogenic	0.60	D
MetaRNN	Benign	0.30	T
MetaSVM	Benign	-0.79	T
PhyloP100		4.1
PrimateAI	Pathogenic	0.94	D
PROVEAN	Benign	-0.79	N
REVEL	Benign	0.093
Sift	Benign	0.38	T
Sift4G	Benign	0.22	T
Polyphen		0.34	B
Vest4		0.23
MutPred		0.39		Gain of helix (P = 0.0128)
MVP		0.25
MPC		0.96
ClinPred		0.99	D
GERP RS		3.8
PromoterAI		0.015	Neutral
Varity_R		0.38
gMVP		0.81
Mutation Taster		=79/21	polymorphism

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

Other links and lift over

dbSNP: rs1416988256; hg19: chr9-96214500;