rs910425

Variant names:

• chr6-170343103-G-A
• rs910425
• NM_032448.3:c.2018-5048G>A

Variant summary

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

The NM_032448.3(FAM120B):​c.2018-5048G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 152,076 control chromosomes in the GnomAD database, including 12,289 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 0.39 (12289 hom., cov: 32)
• Consequence: FAM120B NM_032448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.487
• Publications: 14 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM120B	NM_032448.3	c.2018-5048G>A		intron_variant	Intron 4 of 10	ENST00000476287.4	NP_115824.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM120B	ENST00000476287.4	c.2018-5048G>A		intron_variant	Intron 4 of 10	1	NM_032448.3	ENSP00000417970.1
FAM120B	ENST00000537664.5	c.2087-5048G>A		intron_variant	Intron 4 of 10	2		ENSP00000440125.1
FAM120B	ENST00000630384.2	c.2054-5048G>A		intron_variant	Intron 4 of 10	2		ENSP00000485745.1
FAM120B	ENST00000625626.1	c.14-5048G>A		intron_variant	Intron 2 of 8	2		ENSP00000485793.1

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59576 AN: 151958 Hom.: 12281 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.00807

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.392 AC: 59608 AN: 152076 Hom.: 12289 Cov.: 32 AF XY: 0.393 AC XY: 29175 AN XY: 74328

African (AFR) AF: 0.331 AC: 13728 AN: 41440

American (AMR) AF: 0.430 AC: 6568 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1561 AN: 3468

East Asian (EAS) AF: 0.00847 AC: 44 AN: 5192

South Asian (SAS) AF: 0.403 AC: 1945 AN: 4822

European-Finnish (FIN) AF: 0.432 AC: 4574 AN: 10578

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29855 AN: 67980

Other (OTH) AF: 0.393 AC: 831 AN: 2112

Alfa AF: 0.435 Hom.: 26557

Bravo AF: 0.387

Asia WGS AF: 0.204 AC: 712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.4
DANN	Benign	0.56
PhyloP100		0.49
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: rs910425; hg19: chr6-170652191;