6-170404919-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.91).
• 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

African (AFR) AF: 0.191 AC: 1023 AN: 5348

American (AMR) AF: 0.0716 AC: 396 AN: 5530

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 724 AN: 5918

East Asian (EAS) AF: 0.0410 AC: 496 AN: 12086

South Asian (SAS) AF: 0.0470 AC: 398 AN: 8476

European-Finnish (FIN) AF: 0.0574 AC: 540 AN: 9404

Middle Eastern (MID) AF: 0.153 AC: 126 AN: 822

European-Non Finnish (NFE) AF: 0.0929 AC: 9392 AN: 101056

Other (OTH) AF: 0.103 AC: 1092 AN: 10554

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

African (AFR) AF: 0.219 AC: 9110 AN: 41534

American (AMR) AF: 0.103 AC: 1574 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 503 AN: 3472

East Asian (EAS) AF: 0.0583 AC: 302 AN: 5178

South Asian (SAS) AF: 0.0689 AC: 332 AN: 4818

European-Finnish (FIN) AF: 0.0706 AC: 749 AN: 10608

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.104 AC: 7079 AN: 68024

Other (OTH) AF: 0.140 AC: 297 AN: 2116

Alfa AF: 0.119 Hom.: 532

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
PhyloP100		-0.95
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: rs1274; hg19: chr6-170714007;