rs2024694

Variant names:

• chr6-170311484-C-T
• rs2024694
• NM_032448.3:c.-22+4642C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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=-0.91).
• 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 rank	MANE	Protein	UniProt
FAM120B	NM_032448.3	c.-22+4642C>T		intron_variant	Intron 1 of 10	ENST00000476287.4	NP_115824.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM120B	ENST00000476287.4	c.-22+4642C>T		intron_variant	Intron 1 of 10	1	NM_032448.3	ENSP00000417970.1
FAM120B	ENST00000537664.5	c.49-5886C>T		intron_variant	Intron 1 of 10	2		ENSP00000440125.1
FAM120B	ENST00000630384.2	c.16-5886C>T		intron_variant	Intron 1 of 10	2		ENSP00000485745.1
FAM120B	ENST00000625626.1	c.-90+4642C>T		intron_variant	Intron 1 of 8	2		ENSP00000485793.1

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

African (AFR) AF: 0.219 AC: 9084 AN: 41492

American (AMR) AF: 0.0563 AC: 861 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0421 AC: 146 AN: 3472

East Asian (EAS) AF: 0.0214 AC: 111 AN: 5180

South Asian (SAS) AF: 0.0582 AC: 281 AN: 4826

European-Finnish (FIN) AF: 0.0511 AC: 542 AN: 10604

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0694 AC: 4723 AN: 68014

Other (OTH) AF: 0.0818 AC: 173 AN: 2116

Alfa AF: 0.0762 Hom.: 1102

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
PhyloP100		0.44
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: rs2024694; hg19: chr6-170620572;