Genetic Variant FAM120B:c.*4A>T (chr6-170404594-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032448.3(FAM120B):c.*4A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 1,610,880 control chromosomes in the GnomAD database, including 9,946 homozygotes. 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 0.13 ( 1605 hom., cov: 33)

Exomes 𝑓: 0.10 ( 8341 hom. )

Consequence

FAM120B
NM_032448.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.556

Publications

11 publications found

Variant links:

Genes affected

FAM120B (HGNC:21109): (family with sequence similarity 120 member B) Predicted to be involved in fat cell differentiation and peroxisome proliferator activated receptor signaling pathway. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

FAM120B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM120B	NM_032448.3 link	c.*4A>T		3_prime_UTR_variant	Exon 10 of 11	ENST00000476287.4	NP_115824.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM120B	ENST00000476287.4 link	c.*4A>T		3_prime_UTR_variant	Exon 10 of 11	1	NM_032448.3	ENSP00000417970.1

Frequencies

GnomAD3 genomes

AF:

0.132

AC:

20124

AN:

152026

Hom.:

1602

Cov.:

show subpopulations

Gnomad AFR

AF:

0.219

Gnomad AMI

AF:

0.179

Gnomad AMR

AF:

0.103

Gnomad ASJ

AF:

0.145

Gnomad EAS

AF:

0.0582

Gnomad SAS

AF:

0.0696

Gnomad FIN

AF:

0.0710

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.104

Gnomad OTH

AF:

0.141

GnomAD2 exomes

AF:

0.0956

AC:

23965

AN:

250794

AF XY:

0.0939

show subpopulations

Gnomad AFR exome

AF:

0.222

Gnomad AMR exome

AF:

0.0639

Gnomad ASJ exome

AF:

0.135

Gnomad EAS exome

AF:

0.0582

Gnomad FIN exome

AF:

0.0670

Gnomad NFE exome

AF:

0.102

Gnomad OTH exome

AF:

0.107

GnomAD4 exome

AF:

0.102

AC:

148184

AN:

1458736

Hom.:

8341

Cov.:

AF XY:

0.101

AC XY:

72997

AN XY:

725922

show subpopulations

African (AFR)

AF:

0.225

AC:

7518

AN:

33370

American (AMR)

AF:

0.0672

AC:

3001

AN:

44648

Ashkenazi Jewish (ASJ)

AF:

0.133

AC:

3475

AN:

26088

East Asian (EAS)

AF:

0.0496

AC:

1969

AN:

39674

South Asian (SAS)

AF:

0.0671

AC:

5780

AN:

86116

European-Finnish (FIN)

AF:

0.0663

AC:

3538

AN:

53384

Middle Eastern (MID)

AF:

0.176

AC:

1014

AN:

5756

European-Non Finnish (NFE)

AF:

0.104

AC:

115029

AN:

1109414

Other (OTH)

AF:

0.114

AC:

6860

AN:

60286

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.455

Heterozygous variant carriers

5858

11716

17573

23431

29289

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4246

8492

12738

16984

21230

<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:

0.132

AC:

20155

AN:

152144

Hom.:

1605

Cov.:

AF XY:

0.128

AC XY:

9515

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.220

AC:

9106

AN:

41474

American (AMR)

AF:

0.103

AC:

1575

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.145

AC:

502

AN:

3470

East Asian (EAS)

AF:

0.0583

AC:

302

AN:

5178

South Asian (SAS)

AF:

0.0696

AC:

335

AN:

4812

European-Finnish (FIN)

AF:

0.0710

AC:

753

AN:

10606

Middle Eastern (MID)

AF:

0.163

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.104

AC:

7076

AN:

67992

Other (OTH)

AF:

0.140

AC:

296

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

891

1783

2674

3566

4457

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

222

444

666

888

1110

<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:

0.0635

Hom.:

109

Bravo

AF:

0.140

Asia WGS

AF:

0.0560

AC:

195

AN:

3478

EpiCase

AF:

0.112

EpiControl

AF:

0.115

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.4

(source)

DANN

Benign

0.70

PhyloP100

-0.56

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over