Genetic Variant FAM120B:c.-22+30T>C (chr6-170306872-T-C) – 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.-22+30T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,078 control chromosomes in the GnomAD database, including 9,928 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 0.32 ( 9924 hom., cov: 33)

Exomes 𝑓: 0.24 ( 4 hom. )

Consequence

FAM120B
NM_032448.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.115

Publications

2 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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032448.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FAM120B	NM_032448.3	MANE Select	c.-22+30T>C	intron	N/A	NP_115824.1	Q96EK7-1
FAM120B	NM_001286380.2		c.49-10498T>C	intron	N/A	NP_001273309.1	F5GY05
FAM120B	NM_001286379.2		c.16-10498T>C	intron	N/A	NP_001273308.1	A0A0D9SEJ5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FAM120B	ENST00000476287.4	TSL:1 MANE Select	c.-22+30T>C	intron	N/A	ENSP00000417970.1	Q96EK7-1
FAM120B	ENST00000537664.5	TSL:2	c.49-10498T>C	intron	N/A	ENSP00000440125.1	F5GY05
FAM120B	ENST00000630384.2	TSL:2	c.16-10498T>C	intron	N/A	ENSP00000485745.1	A0A0D9SEJ5

Frequencies

GnomAD3 genomes

AF:

0.324

AC:

49271

AN:

151888

Hom.:

9899

Cov.:

show subpopulations

Gnomad AFR

AF:

0.477

Gnomad AMI

AF:

0.240

Gnomad AMR

AF:

0.282

Gnomad ASJ

AF:

0.202

Gnomad EAS

AF:

0.899

Gnomad SAS

AF:

0.382

Gnomad FIN

AF:

0.216

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.219

Gnomad OTH

AF:

0.291

GnomAD4 exome

AF:

0.243

AC:

AN:

Hom.:

Cov.:

AF XY:

0.296

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.177

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.560

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.325

AC:

49347

AN:

152004

Hom.:

9924

Cov.:

AF XY:

0.326

AC XY:

24194

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.477

AC:

19803

AN:

41478

American (AMR)

AF:

0.283

AC:

4319

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.202

AC:

700

AN:

3472

East Asian (EAS)

AF:

0.899

AC:

4619

AN:

5140

South Asian (SAS)

AF:

0.380

AC:

1828

AN:

4816

European-Finnish (FIN)

AF:

0.216

AC:

2283

AN:

10580

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.219

AC:

14892

AN:

67926

Other (OTH)

AF:

0.296

AC:

625

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1581

3163

4744

6326

7907

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

472

944

1416

1888

2360

<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:

0.126

Hom.:

185

Bravo

AF:

0.339

Asia WGS

AF:

0.653

AC:

2267

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

7.3

(source)

DANN

Benign

0.30

PhyloP100

-0.12

PromoterAI

0.092

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over