Variant chr9-93452646-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_198841.4(FAM120AOS):c.64C>T(p.Leu22Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 1,598,730 control chromosomes in the GnomAD database, including 86,149 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.31 ( 7721 hom., cov: 32)

Exomes 𝑓: 0.33 ( 78428 hom. )

Consequence

FAM120AOS
NM_198841.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.54

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=2.6232004E-4).

BP6

Variant 9-93452646-G-A is Benign according to our data. Variant chr9-93452646-G-A is described in ClinVar as [Benign]. Clinvar id is 1178731.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM120AOS	NM_198841.4 linkuse as main transcript	c.64C>T	p.Leu22Phe	missense_variant	1/3	ENST00000375412.11	NP_942138.2
FAM120A	NM_014612.5 linkuse as main transcript	c.474+257G>A		intron_variant		ENST00000277165.11	NP_055427.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM120AOS	ENST00000375412.11 linkuse as main transcript	c.64C>T	p.Leu22Phe	missense_variant	1/3	1	NM_198841.4	ENSP00000364561	P2
FAM120A	ENST00000277165.11 linkuse as main transcript	c.474+257G>A		intron_variant		1	NM_014612.5	ENSP00000277165	P3	Q9NZB2-1

Frequencies

GnomAD3 genomes

AF:

0.311

AC:

47254

AN:

151980

Hom.:

7718

Cov.:

show subpopulations

Gnomad AFR

AF:

0.242

Gnomad AMI

AF:

0.295

Gnomad AMR

AF:

0.336

Gnomad ASJ

AF:

0.315

Gnomad EAS

AF:

0.440

Gnomad SAS

AF:

0.179

Gnomad FIN

AF:

0.360

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.340

Gnomad OTH

AF:

0.312

GnomAD3 exomes

AF:

0.319

AC:

74215

AN:

232528

Hom.:

12574

AF XY:

0.315

AC XY:

40447

AN XY:

128468

show subpopulations

Gnomad AFR exome

AF:

0.230

Gnomad AMR exome

AF:

0.346

Gnomad ASJ exome

AF:

0.310

Gnomad EAS exome

AF:

0.450

Gnomad SAS exome

AF:

0.184

Gnomad FIN exome

AF:

0.361

Gnomad NFE exome

AF:

0.335

Gnomad OTH exome

AF:

0.322

GnomAD4 exome

AF:

0.326

AC:

471206

AN:

1446634

Hom.:

78428

Cov.:

AF XY:

0.323

AC XY:

232314

AN XY:

720166

show subpopulations

Gnomad4 AFR exome

AF:

0.232

Gnomad4 AMR exome

AF:

0.342

Gnomad4 ASJ exome

AF:

0.313

Gnomad4 EAS exome

AF:

0.463

Gnomad4 SAS exome

AF:

0.192

Gnomad4 FIN exome

AF:

0.361

Gnomad4 NFE exome

AF:

0.334

Gnomad4 OTH exome

AF:

0.310

GnomAD4 genome

AF:

0.311

AC:

47267

AN:

152096

Hom.:

7721

Cov.:

AF XY:

0.311

AC XY:

23086

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.241

Gnomad4 AMR

AF:

0.336

Gnomad4 ASJ

AF:

0.315

Gnomad4 EAS

AF:

0.440

Gnomad4 SAS

AF:

0.181

Gnomad4 FIN

AF:

0.360

Gnomad4 NFE

AF:

0.340

Gnomad4 OTH

AF:

0.308

Alfa

AF:

0.328

Hom.:

10762

Bravo

AF:

0.311

TwinsUK

AF:

0.329

AC:

1219

ALSPAC

AF:

0.322

AC:

1242

ESP6500AA

AF:

0.218

AC:

862

ESP6500EA

AF:

0.302

AC:

2380

ExAC

AF:

0.313

AC:

36903

Asia WGS

AF:

0.282

AC:

979

AN:

3478

EpiCase

AF:

0.329

EpiControl

AF:

0.329

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.25

BayesDel_addAF

Benign

-0.77

BayesDel_noAF

Benign

-0.73

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.0043

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.026

LIST_S2

Benign

0.33

MetaRNN

Benign

0.00026

MetaSVM

Benign

-0.95

MutationAssessor

Benign

0.0

MutationTaster

Benign

1.0

P;P;P;P;P

PrimateAI

Benign

0.25

PROVEAN

Benign

-1.4

REVEL

Benign

0.049

Sift

Benign

0.26

Polyphen

0.048

Vest4

0.047

MPC

0.85

ClinPred

0.0090

GERP RS

-6.6

Varity_R

0.054

gMVP

0.028

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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