9-93452218-G-A

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014612.5(FAM120A):​c.303G>A​(p.Glu101Glu) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000206 in 1,459,272 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: FAM120A NM_014612.5 synonymous
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).

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>A	p.Glu101Glu	synonymous	Exon 1 of 18	NP_055427.2
	FAM120AOS	NM_198841.4	MANE Select	c.492C>T	p.Phe164Phe	synonymous	Exon 1 of 3	NP_942138.2	Q5T036
	FAM120A	NM_001439102.1		c.303G>A	p.Glu101Glu	synonymous	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>A	p.Glu101Glu	synonymous	Exon 1 of 18	ENSP00000277165.5	Q9NZB2-1
	FAM120AOS	ENST00000375412.11	TSL:1 MANE Select	c.492C>T	p.Phe164Phe	synonymous	Exon 1 of 3	ENSP00000364561.5	Q5T036
	FAM120A	ENST00000375389.7	TSL:1	c.303G>A	p.Glu101Glu	synonymous	Exon 1 of 9	ENSP00000364538.3	Q9NZB2-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000206 AC: 3 AN: 1459272 Hom.: 0 Cov.: 34 AF XY: 0.00000276 AC XY: 2 AN XY: 725902

African (AFR) AF: 0.0000598 AC: 2 AN: 33456

American (AMR) AF: 0.00 AC: 0 AN: 44600

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26076

East Asian (EAS) AF: 0.00 AC: 0 AN: 39664

South Asian (SAS) AF: 0.00 AC: 0 AN: 86064

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51750

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5766

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1111600

Other (OTH) AF: 0.0000166 AC: 1 AN: 60296

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	14
DANN	Uncertain	0.98
PhyloP100		4.1
PromoterAI		-0.075	Neutral

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;