ENST00000423591.5:c.-435G>T

Variant names:

• chr9-93451539-C-A
• rs371621692
• ENST00000423591.5:c.-435G>T

Variant summary

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

The ENST00000423591.5(FAM120AOS):​c.-435G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000665 in 150,332 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: 𝑓 0.0000067 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FAM120AOS ENST00000423591.5 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.43
• Publications: 0 publications found

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]

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)

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=-0.77).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000423591.5. 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
	FAM120AOS	NM_198841.4	MANE Select	c.563+608G>T		intron	N/A	NP_942138.2	Q5T036
	FAM120AOS	NM_001322224.3		c.-435G>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 3	NP_001309153.1	E9PCY8
	FAM120AOS	NM_001322224.3		c.-435G>T		5_prime_UTR	Exon 1 of 3	NP_001309153.1	E9PCY8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM120AOS	ENST00000423591.5	TSL:1	c.-435G>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 3	ENSP00000414298.1	E9PCY8
	FAM120AOS	ENST00000423591.5	TSL:1	c.-435G>T		5_prime_UTR	Exon 1 of 3	ENSP00000414298.1	E9PCY8
	FAM120AOS	ENST00000375412.11	TSL:1 MANE Select	c.563+608G>T		intron	N/A	ENSP00000364561.5	Q5T036

Frequencies

GnomAD3 genomes AF: 0.00000665 AC: 1 AN: 150332 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000660

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 838858 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 387724

African (AFR) AF: 0.00 AC: 0 AN: 16008

American (AMR) AF: 0.00 AC: 0 AN: 1124

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5362

East Asian (EAS) AF: 0.00 AC: 0 AN: 3942

South Asian (SAS) AF: 0.00 AC: 0 AN: 16760

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 558

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1662

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 765800

Other (OTH) AF: 0.00 AC: 0 AN: 27642

GnomAD4 genome AF: 0.00000665 AC: 1 AN: 150332 Hom.: 0 Cov.: 32 AF XY: 0.0000137 AC XY: 1 AN XY: 73250

African (AFR) AF: 0.00 AC: 0 AN: 41248

American (AMR) AF: 0.0000660 AC: 1 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3422

East Asian (EAS) AF: 0.00 AC: 0 AN: 5156

South Asian (SAS) AF: 0.00 AC: 0 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10328

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 314

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 66906

Other (OTH) AF: 0.00 AC: 0 AN: 2058

Alfa AF: 0.00 Hom.: 1

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.1
DANN	Benign	0.60
PhyloP100		-4.4
PromoterAI		-0.10	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.0

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: rs371621692; hg19: chr9-96213821;