rs2103816

chr6-170366925-T-A

Variant summary

Our verdict is Benign. Variant got -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

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=-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/exons	MANE	UniProt
FAM120B	NM_032448.3	c.2283+8607T>A		intron_variant		ENST00000476287.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM120B	ENST00000476287.4	c.2283+8607T>A		intron_variant		1	NM_032448.3	A2
FAM120B	ENST00000537664.5	c.2352+8607T>A		intron_variant		2		A2
FAM120B	ENST00000625626.1	c.279+8607T>A		intron_variant		2		P2
FAM120B	ENST00000630384.2	c.2319+8607T>A		intron_variant		2		A2

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

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.0425

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.588

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

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: rs2103816; hg19: chr6-170676013; COSMIC: COSV53002470;