rs2024694

chr6-170311484-C-T

Variant summary

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

The NM_032448.3(FAM120B):c.-22+4642C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,200 control chromosomes in the GnomAD database, including 1,255 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 0.11 (1255 hom., cov: 33)
• Consequence: FAM120B NM_032448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.444

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM120B	NM_032448.3	c.-22+4642C>T		intron_variant		ENST00000476287.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM120B	ENST00000476287.4	c.-22+4642C>T		intron_variant		1	NM_032448.3	A2
FAM120B	ENST00000537664.5	c.49-5886C>T		intron_variant		2		A2
FAM120B	ENST00000625626.1	c.-90+4642C>T		intron_variant		2		P2
FAM120B	ENST00000630384.2	c.16-5886C>T		intron_variant		2		A2

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15953 AN: 152082 Hom.: 1246 Cov.: 33

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.0639

Gnomad AMR AF: 0.0564

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.0592

Gnomad FIN AF: 0.0511

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0695

Gnomad OTH AF: 0.0783

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

GnomAD4 genome AF: 0.105 AC: 15988 AN: 152200 Hom.: 1255 Cov.: 33 AF XY: 0.100 AC XY: 7455 AN XY: 74408

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.0563

Gnomad4 ASJ AF: 0.0421

Gnomad4 EAS AF: 0.0214

Gnomad4 SAS AF: 0.0582

Gnomad4 FIN AF: 0.0511

Gnomad4 NFE AF: 0.0694

Gnomad4 OTH AF: 0.0818

Alfa AF: 0.0715 Hom.: 654

Bravo AF: 0.108

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.6
Dann	Benign	0.57

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: rs2024694; hg19: chr6-170620572;