rs9366215

chr6-170365278-T-C

Variant summary

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

The NM_032448.3(FAM120B):c.2283+6960T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 152,144 control chromosomes in the GnomAD database, including 10,735 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 0.34 (10735 hom., cov: 33)
• Consequence: FAM120B NM_032448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87

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=-1.03).
• 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/exons	MANE	UniProt
FAM120B	NM_032448.3	c.2283+6960T>C		intron_variant		ENST00000476287.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM120B	ENST00000476287.4	c.2283+6960T>C		intron_variant		1	NM_032448.3	A2
FAM120B	ENST00000537664.5	c.2352+6960T>C		intron_variant		2		A2
FAM120B	ENST00000625626.1	c.279+6960T>C		intron_variant		2		P2
FAM120B	ENST00000630384.2	c.2319+6960T>C		intron_variant		2		A2

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52402 AN: 152026 Hom.: 10708 Cov.: 33

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.345 AC: 52483 AN: 152144 Hom.: 10735 Cov.: 33 AF XY: 0.346 AC XY: 25726 AN XY: 74374

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.325

Alfa AF: 0.301 Hom.: 1267

Bravo AF: 0.359

Asia WGS AF: 0.663 AC: 2301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.12
Dann	Benign	0.25

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: rs9366215; hg19: chr6-170674366;