rs1274

Variant names:

• chr6-170404919-T-C
• rs1274
• NM_032448.3:c.*168T>C

Variant summary

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

The NM_032448.3(FAM120B):​c.*168T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 311,440 control chromosomes in the GnomAD database, including 2,295 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 0.13 (1602 hom., cov: 33)
  • Exomes 𝑓: 0.089 (693 hom.)
• Consequence: FAM120B NM_032448.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.955

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 = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM120B	NM_032448.3	c.*168T>C		3_prime_UTR_variant	Exon 11 of 11	ENST00000476287.4	NP_115824.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM120B	ENST00000476287.4	c.*168T>C		3_prime_UTR_variant	Exon 11 of 11	1	NM_032448.3	ENSP00000417970.1

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20127 AN: 152128 Hom.: 1599 Cov.: 33

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0582

Gnomad SAS AF: 0.0689

Gnomad FIN AF: 0.0706

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.141

GnomAD4 exome AF: 0.0891 AC: 14187 AN: 159194 Hom.: 693 Cov.: 0 AF XY: 0.0892 AC XY: 7264 AN XY: 81396

Gnomad4 AFR exome AF: 0.191

Gnomad4 AMR exome AF: 0.0716

Gnomad4 ASJ exome AF: 0.122

Gnomad4 EAS exome AF: 0.0410

Gnomad4 SAS exome AF: 0.0470

Gnomad4 FIN exome AF: 0.0574

Gnomad4 NFE exome AF: 0.0929

Gnomad4 OTH exome AF: 0.103

GnomAD4 genome AF: 0.132 AC: 20158 AN: 152246 Hom.: 1602 Cov.: 33 AF XY: 0.128 AC XY: 9513 AN XY: 74446

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.0583

Gnomad4 SAS AF: 0.0689

Gnomad4 FIN AF: 0.0706

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.140

Alfa AF: 0.116 Hom.: 410

Bravo AF: 0.140

Asia WGS AF: 0.0560 AC: 195 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	0.87
DANN	Benign	0.52

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: rs1274; hg19: chr6-170714007;