NM_032448.3:c.2284-350A>G

Variant names:

• chr6-170387937-A-G
• rs958998
• NM_032448.3:c.2284-350A>G

Variant summary

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

The NM_032448.3(FAM120B):​c.2284-350A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 152,152 control chromosomes in the GnomAD database, including 47,616 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 0.79 (47616 hom., cov: 32)
• Consequence: FAM120B NM_032448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111
• Publications: 8 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]

LOC124901474 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM120B	NM_032448.3	c.2284-350A>G		intron_variant	Intron 6 of 10	ENST00000476287.4	NP_115824.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM120B	ENST00000476287.4	c.2284-350A>G		intron_variant	Intron 6 of 10	1	NM_032448.3	ENSP00000417970.1
FAM120B	ENST00000537664.5	c.2353-350A>G		intron_variant	Intron 6 of 10	2		ENSP00000440125.1
FAM120B	ENST00000630384.2	c.2320-350A>G		intron_variant	Intron 6 of 10	2		ENSP00000485745.1
FAM120B	ENST00000625626.1	c.280-350A>G		intron_variant	Intron 4 of 8	2		ENSP00000485793.1

Frequencies

GnomAD3 genomes AF: 0.790 AC: 120114 AN: 152034 Hom.: 47582 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.790 AC: 120205 AN: 152152 Hom.: 47616 Cov.: 32 AF XY: 0.793 AC XY: 58989 AN XY: 74388

African (AFR) AF: 0.789 AC: 32759 AN: 41500

American (AMR) AF: 0.818 AC: 12509 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2701 AN: 3472

East Asian (EAS) AF: 0.942 AC: 4864 AN: 5164

South Asian (SAS) AF: 0.883 AC: 4262 AN: 4824

European-Finnish (FIN) AF: 0.757 AC: 8010 AN: 10588

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.775 AC: 52679 AN: 67998

Other (OTH) AF: 0.781 AC: 1648 AN: 2110

Alfa AF: 0.782 Hom.: 204384

Bravo AF: 0.792

Asia WGS AF: 0.920 AC: 3199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.88
DANN	Benign	0.47
PhyloP100		0.11
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: rs958998; hg19: chr6-170697025;