chr6-170397106-C-A

Position:

• chr6-170397106-C-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM120B	NM_032448.3	c.2692+1527C>A		intron_variant		ENST00000476287.4	NP_115824.1
LOC124901475	XR_007059898.1	n.1521C>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM120B	ENST00000476287.4	c.2692+1527C>A		intron_variant		1	NM_032448.3	ENSP00000417970	A2
FAM120B	ENST00000537664.5	c.2761+1527C>A		intron_variant		2		ENSP00000440125	A2
FAM120B	ENST00000625626.1	c.688+1527C>A		intron_variant		2		ENSP00000485793	P2
FAM120B	ENST00000630384.2	c.2728+1527C>A		intron_variant		2		ENSP00000485745	A2

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

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.0423

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.549

Alfa AF: 0.608 Hom.: 11659

Bravo AF: 0.536

Asia WGS AF: 0.291 AC: 1016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.86
DANN	Benign	0.55
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs727619; hg19: chr6-170706194;