rs1416988256

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-93452218-G-T
• chr9-93452218-G-A
• chr9-93452218-G-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>T​(p.Glu101Asp) variant causes a missense 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. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: FAM120A NM_014612.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• 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=0.28842598).

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>T	p.Glu101Asp	missense	Exon 1 of 18	NP_055427.2
	FAM120AOS	NM_198841.4	MANE Select	c.492C>A	p.Phe164Leu	missense	Exon 1 of 3	NP_942138.2	Q5T036
	FAM120A	NM_001439102.1		c.303G>T	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>T	p.Glu101Asp	missense	Exon 1 of 18	ENSP00000277165.5	Q9NZB2-1
	FAM120AOS	ENST00000375412.11	TSL:1 MANE Select	c.492C>A	p.Phe164Leu	missense	Exon 1 of 3	ENSP00000364561.5	Q5T036
	FAM120A	ENST00000375389.7	TSL:1	c.303G>T	p.Glu101Asp	missense	Exon 1 of 9	ENSP00000364538.3	Q9NZB2-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.0000125 AC: 3 AN: 240046 AF XY: 0.0000228

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000168

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000206 AC: 3 AN: 1459272 Hom.: 0 Cov.: 34 AF XY: 0.00000413 AC XY: 3 AN XY: 725902

African (AFR) AF: 0.00 AC: 0 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: 0.0000756 AC: 3 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: 0.00 AC: 0 AN: 60296

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.33
BayesDel_addAF	Benign	-0.31	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	0.88	D
LIST_S2	Uncertain	0.94	D
M_CAP	Pathogenic	0.61	D
MetaRNN	Benign	0.29	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		0.26
MPC		0.96
ClinPred		0.97	D
GERP RS		3.8
PromoterAI		-0.013	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;