chr6-170397106-C-A

Variant names:

• chr6-170397106-C-A
• rs727619
• NM_032448.3:c.2692+1527C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032448.3(FAM120B):​c.2692+1527C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 152,122 control chromosomes in the GnomAD database, including 24,753 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 0.55 (24753 hom., cov: 34)
• Consequence: FAM120B NM_032448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 8 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]

LOC124901475 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032448.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM120B	NM_032448.3	MANE Select	c.2692+1527C>A		intron	N/A	NP_115824.1	Q96EK7-1
	FAM120B	NM_001286380.2		c.2761+1527C>A		intron	N/A	NP_001273309.1	F5GY05
	FAM120B	NM_001286379.2		c.2728+1527C>A		intron	N/A	NP_001273308.1	A0A0D9SEJ5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM120B	ENST00000476287.4	TSL:1 MANE Select	c.2692+1527C>A		intron	N/A	ENSP00000417970.1	Q96EK7-1
	FAM120B	ENST00000537664.5	TSL:2	c.2761+1527C>A		intron	N/A	ENSP00000440125.1	F5GY05
	FAM120B	ENST00000630384.2	TSL:2	c.2728+1527C>A		intron	N/A	ENSP00000485745.1	A0A0D9SEJ5

Frequencies

GnomAD3 genomes AF: 0.553 AC: 84017 AN: 152004 Hom.: 24748 Cov.: 34

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.0418

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.553 AC: 84056 AN: 152122 Hom.: 24753 Cov.: 34 AF XY: 0.555 AC XY: 41244 AN XY: 74358

African (AFR) AF: 0.407 AC: 16882 AN: 41492

American (AMR) AF: 0.601 AC: 9183 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2195 AN: 3472

East Asian (EAS) AF: 0.0423 AC: 219 AN: 5176

South Asian (SAS) AF: 0.535 AC: 2580 AN: 4818

European-Finnish (FIN) AF: 0.687 AC: 7271 AN: 10580

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43862 AN: 67982

Other (OTH) AF: 0.549 AC: 1159 AN: 2112

Alfa AF: 0.611 Hom.: 17302

Bravo AF: 0.536

Asia WGS AF: 0.291 AC: 1016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.86
DANN	Benign	0.55
PhyloP100		-0.12
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs727619; hg19: chr6-170706194;