rs2103816

Variant names:

• chr6-170366925-T-A
• rs2103816
• NM_032448.3:c.2283+8607T>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.2283+8607T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 151,922 control chromosomes in the GnomAD database, including 26,926 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 0.58 (26926 hom., cov: 30)
• Consequence: FAM120B NM_032448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 9 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM120B	NM_032448.3	c.2283+8607T>A		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.2283+8607T>A		intron_variant	Intron 6 of 10	1	NM_032448.3	ENSP00000417970.1
FAM120B	ENST00000537664.5	c.2352+8607T>A		intron_variant	Intron 6 of 10	2		ENSP00000440125.1
FAM120B	ENST00000630384.2	c.2319+8607T>A		intron_variant	Intron 6 of 10	2		ENSP00000485745.1
FAM120B	ENST00000625626.1	c.279+8607T>A		intron_variant	Intron 4 of 8	2		ENSP00000485793.1

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87379 AN: 151802 Hom.: 26921 Cov.: 30

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.0421

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.575 AC: 87415 AN: 151922 Hom.: 26926 Cov.: 30 AF XY: 0.577 AC XY: 42860 AN XY: 74250

African (AFR) AF: 0.412 AC: 17058 AN: 41414

American (AMR) AF: 0.627 AC: 9567 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2286 AN: 3468

East Asian (EAS) AF: 0.0425 AC: 220 AN: 5172

South Asian (SAS) AF: 0.552 AC: 2652 AN: 4800

European-Finnish (FIN) AF: 0.714 AC: 7524 AN: 10542

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46146 AN: 67950

Other (OTH) AF: 0.588 AC: 1239 AN: 2108

Alfa AF: 0.635 Hom.: 3881

Bravo AF: 0.559

Asia WGS AF: 0.299 AC: 1043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.2
DANN	Benign	0.85
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: rs2103816; hg19: chr6-170676013; COSMIC: COSV53002470;