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

Variant summary

Our verdict is Benign. The variant received -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

Publications

0 publications found

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 Gene-Disease associations (from GenCC):

Tourette syndrome
Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

FAM120A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001322224.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FAM120AOS	NM_198841.4	MANE Select	c.563+608G>A	intron	N/A	NP_942138.2	Q5T036
FAM120AOS	NM_001322224.3		c.-435G>A	5_prime_UTR	Exon 1 of 3	NP_001309153.1	E9PCY8
FAM120AOS	NR_136232.3		n.70G>A	non_coding_transcript_exon	Exon 1 of 4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FAM120AOS	ENST00000423591.5	TSL:1	c.-435G>A	5_prime_UTR	Exon 1 of 3	ENSP00000414298.1	E9PCY8
FAM120AOS	ENST00000375412.11	TSL:1 MANE Select	c.563+608G>A	intron	N/A	ENSP00000364561.5	Q5T036
FAM120AOS	ENST00000476484.5	TSL:1	n.-435G>A	non_coding_transcript_exon	Exon 1 of 4	ENSP00000429212.1	E5RJ17

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

African (AFR)

AF:

0.0610

AC:

977

AN:

16008

American (AMR)

AF:

0.00712

AC:

AN:

1124

Ashkenazi Jewish (ASJ)

AF:

0.00466

AC:

AN:

5362

East Asian (EAS)

AF:

0.00913

AC:

AN:

3942

South Asian (SAS)

AF:

0.0332

AC:

556

AN:

16760

European-Finnish (FIN)

AF:

0.00

AC:

AN:

558

Middle Eastern (MID)

AF:

0.00722

AC:

AN:

1662

European-Non Finnish (NFE)

AF:

0.000713

AC:

546

AN:

765798

Other (OTH)

AF:

0.00760

AC:

210

AN:

27642

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

154

309

463

618

772

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

176

264

352

440

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0190

AC:

2853

AN:

150434

Hom.:

Cov.:

AF XY:

0.0193

AC XY:

1416

AN XY:

73362

show subpopulations

African (AFR)

AF:

0.0591

AC:

2446

AN:

41360

American (AMR)

AF:

0.00712

AC:

108

AN:

15178

Ashkenazi Jewish (ASJ)

AF:

0.00321

AC:

AN:

3422

East Asian (EAS)

AF:

0.00895

AC:

AN:

5140

South Asian (SAS)

AF:

0.0325

AC:

157

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10328

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.000777

AC:

AN:

66896

Other (OTH)

AF:

0.0135

AC:

AN:

2080

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

135

270

405

540

675

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

102

136

170

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000499

Hom.:

Bravo

AF:

0.0207

Asia WGS

AF:

0.0270

AC:

AN:

3408

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

6.0

(source)

DANN

Benign

0.85

PhyloP100

-4.4

PromoterAI

-0.092

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.0

Mutation Taster

=100/0

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over