Genetic Variant FAM120B:c.-22+30T>C (chr6-170306872-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -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

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM120B	NM_032448.3 link	c.-22+30T>C		intron_variant	Intron 1 of 10	ENST00000476287.4	NP_115824.1	Q96EK7-1B4DSS4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
FAM120B	ENST00000476287.4 link	c.-22+30T>C	intron_variant	Intron 1 of 10	1	NM_032448.3	ENSP00000417970.1	Q96EK7-1
FAM120B	ENST00000537664.5 link	c.49-10498T>C	intron_variant	Intron 1 of 10	2		ENSP00000440125.1	F5GY05
FAM120B	ENST00000630384.2 link	c.16-10498T>C	intron_variant	Intron 1 of 10	2		ENSP00000485745.1	A0A0D9SEJ5
FAM120B	ENST00000625626.1 link	c.-90+30T>C	intron_variant	Intron 1 of 8	2		ENSP00000485793.1	Q96EK7-3

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

Gnomad4 AFR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.177

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.325

AC:

49347

AN:

152004

Hom.:

9924

Cov.:

AF XY:

0.326

AC XY:

24194

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.477

Gnomad4 AMR

AF:

0.283

Gnomad4 ASJ

AF:

0.202

Gnomad4 EAS

AF:

0.899

Gnomad4 SAS

AF:

0.380

Gnomad4 FIN

AF:

0.216

Gnomad4 NFE

AF:

0.219

Gnomad4 OTH

AF:

0.296

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

7.3

DANN

Benign

0.30

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over