rs958997

Variant names:

• chr6-170388111-G-T
• rs958997
• NM_032448.3:c.2284-176G>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.2284-176G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.874 in 152,222 control chromosomes in the GnomAD database, including 58,290 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 0.87 (58290 hom., cov: 32)
• Consequence: FAM120B NM_032448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 2 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]

LOC124901474 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM120B	NM_032448.3	c.2284-176G>T		intron_variant	Intron 6 of 10	ENST00000476287.4	NP_115824.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM120B	ENST00000476287.4	c.2284-176G>T		intron_variant	Intron 6 of 10	1	NM_032448.3	ENSP00000417970.1
FAM120B	ENST00000537664.5	c.2353-176G>T		intron_variant	Intron 6 of 10	2		ENSP00000440125.1
FAM120B	ENST00000630384.2	c.2320-176G>T		intron_variant	Intron 6 of 10	2		ENSP00000485745.1
FAM120B	ENST00000625626.1	c.280-176G>T		intron_variant	Intron 4 of 8	2		ENSP00000485793.1

Frequencies

GnomAD3 genomes AF: 0.874 AC: 132918 AN: 152104 Hom.: 58254 Cov.: 32

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.824

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.874 AC: 133009 AN: 152222 Hom.: 58290 Cov.: 32 AF XY: 0.877 AC XY: 65320 AN XY: 74442

African (AFR) AF: 0.803 AC: 33314 AN: 41512

American (AMR) AF: 0.898 AC: 13736 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.856 AC: 2969 AN: 3468

East Asian (EAS) AF: 0.942 AC: 4875 AN: 5174

South Asian (SAS) AF: 0.931 AC: 4489 AN: 4820

European-Finnish (FIN) AF: 0.929 AC: 9868 AN: 10620

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.896 AC: 60942 AN: 68020

Other (OTH) AF: 0.865 AC: 1823 AN: 2108

Alfa AF: 0.887 Hom.: 7733

Bravo AF: 0.868

Asia WGS AF: 0.946 AC: 3290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.60
DANN	Benign	0.33
PhyloP100		-1.2
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: rs958997; hg19: chr6-170697199;