Genetic Variant FAM120AOS:c.-435G>A (chr9-93451539-C-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001322224.3(FAM120AOS):c.-435G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00528 in 989,290 control chromosomes in the GnomAD database, including 150 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.019 ( 92 hom., cov: 32)

Exomes 𝑓: 0.0028 ( 58 hom. )

Consequence

FAM120AOS
NM_001322224.3 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.43

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 9-93451539-C-T is Benign according to our data. Variant chr9-93451539-C-T is described in ClinVar as [Benign]. Clinvar id is 1241520.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM120AOS	NM_198841.4 link	c.563+608G>A		intron_variant	Intron 1 of 2	ENST00000375412.11	NP_942138.2	Q5T036
FAM120A	NM_014612.5 link	c.-377C>T		upstream_gene_variant		ENST00000277165.11	NP_055427.2	Q9NZB2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM120AOS	ENST00000375412.11 link	c.563+608G>A		intron_variant	Intron 1 of 2	1	NM_198841.4	ENSP00000364561.5		Q5T036
FAM120A	ENST00000277165.11 link	c.-377C>T		upstream_gene_variant		1	NM_014612.5	ENSP00000277165.5		Q9NZB2-1

Frequencies

GnomAD3 genomes

AF:

0.0189

AC:

2838

AN:

150330

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0589

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.00712

Gnomad ASJ

AF:

0.00321

Gnomad EAS

AF:

0.00892

Gnomad SAS

AF:

0.0325

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.000777

Gnomad OTH

AF:

0.0136

GnomAD4 exome

AF:

0.00283

AC:

2370

AN:

838856

Hom.:

Cov.:

AF XY:

0.00282

AC XY:

1095

AN XY:

387724

show subpopulations

Gnomad4 AFR exome

AF:

0.0610

Gnomad4 AMR exome

AF:

0.00712

Gnomad4 ASJ exome

AF:

0.00466

Gnomad4 EAS exome

AF:

0.00913

Gnomad4 SAS exome

AF:

0.0332

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000713

Gnomad4 OTH exome

AF:

0.00760

GnomAD4 genome

AF:

0.0190

AC:

2853

AN:

150434

Hom.:

Cov.:

AF XY:

0.0193

AC XY:

1416

AN XY:

73362

show subpopulations

Gnomad4 AFR

AF:

0.0591

Gnomad4 AMR

AF:

0.00712

Gnomad4 ASJ

AF:

0.00321

Gnomad4 EAS

AF:

0.00895

Gnomad4 SAS

AF:

0.0325

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000777

Gnomad4 OTH

AF:

0.0135

Alfa

AF:

0.000499

Hom.:

Bravo

AF:

0.0207

Asia WGS

AF:

0.0270

AC:

AN:

3408

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jul 05, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

6.0

DANN

Benign

0.85

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over