chr6-170389425-A-G

Position:

• chr6-170389425-A-G

Variant summary

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

The NM_032448.3(FAM120B):​c.2490+932A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 152,150 control chromosomes in the GnomAD database, including 58,619 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 0.88 (58619 hom., cov: 31)
• Consequence: FAM120B NM_032448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• 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/exons	MANE	Protein	UniProt
FAM120B	NM_032448.3	c.2490+932A>G		intron_variant		ENST00000476287.4	NP_115824.1
LOC124901474	XR_007059897.1	n.137-1846T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM120B	ENST00000476287.4	c.2490+932A>G		intron_variant		1	NM_032448.3	ENSP00000417970	A2
FAM120B	ENST00000537664.5	c.2559+932A>G		intron_variant		2		ENSP00000440125	A2
FAM120B	ENST00000625626.1	c.486+932A>G		intron_variant		2		ENSP00000485793	P2
FAM120B	ENST00000630384.2	c.2526+932A>G		intron_variant		2		ENSP00000485745	A2

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133281 AN: 152032 Hom.: 58583 Cov.: 31

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.865

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

GnomAD4 genome AF: 0.877 AC: 133373 AN: 152150 Hom.: 58619 Cov.: 31 AF XY: 0.880 AC XY: 65485 AN XY: 74388

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.900

Gnomad4 ASJ AF: 0.860

Gnomad4 EAS AF: 0.942

Gnomad4 SAS AF: 0.931

Gnomad4 FIN AF: 0.929

Gnomad4 NFE AF: 0.897

Gnomad4 OTH AF: 0.867

Alfa AF: 0.892 Hom.: 7506

Bravo AF: 0.871

Asia WGS AF: 0.947 AC: 3293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.48

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: rs2144245; hg19: chr6-170698513;