6-170374153-G-C

Variant names:

• chr6-170374153-G-C
• rs1022615
• NM_032448.3:c.2284-14134G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032448.3(FAM120B):​c.2284-14134G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.919 in 152,326 control chromosomes in the GnomAD database, including 64,361 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 0.92 (64361 hom., cov: 34)
• Consequence: FAM120B NM_032448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 3 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.947 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM120B	NM_032448.3	MANE Select	c.2284-14134G>C		intron	N/A	NP_115824.1
	FAM120B	NM_001286380.2		c.2353-14134G>C		intron	N/A	NP_001273309.1
	FAM120B	NM_001286379.2		c.2320-14134G>C		intron	N/A	NP_001273308.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM120B	ENST00000476287.4	TSL:1 MANE Select	c.2284-14134G>C		intron	N/A	ENSP00000417970.1
	FAM120B	ENST00000537664.5	TSL:2	c.2353-14134G>C		intron	N/A	ENSP00000440125.1
	FAM120B	ENST00000630384.2	TSL:2	c.2320-14134G>C		intron	N/A	ENSP00000485745.1

Frequencies

GnomAD3 genomes AF: 0.919 AC: 139839 AN: 152208 Hom.: 64306 Cov.: 34

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.928

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.894

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.919 AC: 139954 AN: 152326 Hom.: 64361 Cov.: 34 AF XY: 0.921 AC XY: 68571 AN XY: 74482

African (AFR) AF: 0.955 AC: 39690 AN: 41572

American (AMR) AF: 0.916 AC: 14025 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2987 AN: 3472

East Asian (EAS) AF: 0.942 AC: 4886 AN: 5186

South Asian (SAS) AF: 0.933 AC: 4506 AN: 4830

European-Finnish (FIN) AF: 0.928 AC: 9852 AN: 10614

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.898 AC: 61114 AN: 68032

Other (OTH) AF: 0.895 AC: 1888 AN: 2110

Alfa AF: 0.915 Hom.: 2109

Bravo AF: 0.919

Asia WGS AF: 0.957 AC: 3329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.32
DANN	Benign	0.48
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1022615; hg19: chr6-170683241;