6-170374153-G-C

Position:

• chr6-170374153-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000476287.4(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 ENST00000476287.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM120B	NM_032448.3	c.2284-14134G>C		intron_variant		ENST00000476287.4	NP_115824.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM120B	ENST00000476287.4	c.2284-14134G>C		intron_variant		1	NM_032448.3	ENSP00000417970	A2
FAM120B	ENST00000537664.5	c.2353-14134G>C		intron_variant		2		ENSP00000440125	A2
FAM120B	ENST00000625626.1	c.280-14134G>C		intron_variant		2		ENSP00000485793	P2
FAM120B	ENST00000630384.2	c.2320-14134G>C		intron_variant		2		ENSP00000485745	A2

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

Gnomad4 AFR AF: 0.955

Gnomad4 AMR AF: 0.916

Gnomad4 ASJ AF: 0.860

Gnomad4 EAS AF: 0.942

Gnomad4 SAS AF: 0.933

Gnomad4 FIN AF: 0.928

Gnomad4 NFE AF: 0.898

Gnomad4 OTH AF: 0.895

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.32
DANN	Benign	0.48

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

LitVar

Other links and lift over

dbSNP: rs1022615; hg19: chr6-170683241;