NM_001382779.1:c.26_32dupGGGCCGG

Variant names:

• chr16-30925767-A-AGCCGGGG
• rs2055582969
• NM_001382779.1:c.26_32dupGGGCCGG

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001382779.1(FBXL19):​c.26_32dupGGGCCGG​(p.Ala12GlyfsTer20) variant causes a frameshift change. The variant allele was found at a frequency of 0.0000015 in 1,331,922 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000015 (0 hom.)
• Consequence: FBXL19 NM_001382779.1 frameshift
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.70
• Publications: 0 publications found

Genes affected

FBXL19 (HGNC:25300): (F-box and leucine rich repeat protein 19) This gene encodes a member of the Skp1-Cullin-F-box family of E3 ubiquitin ligases. The encoded protein is reported to bind to the transmembrane receptor interleukin 1 receptor-like 1 and regulate its ubiquitination and degradation. This protein has been linked to the regulation of pulmonary inflammation and psoriasis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001382779.1. 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
	FBXL19	NM_001382779.1	MANE Select	c.26_32dupGGGCCGG	p.Ala12GlyfsTer20	frameshift	Exon 2 of 11	NP_001369708.1	H3BPZ0
	FBXL19	NM_001099784.3		c.86_92dupGGGCCGG	p.Ala32GlyfsTer20	frameshift	Exon 2 of 11	NP_001093254.2	Q6PCT2-1
	FBXL19	NM_001382780.1		c.92_98dupGGGCCGG	p.Ala34GlyfsTer20	frameshift	Exon 2 of 11	NP_001369709.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FBXL19	ENST00000338343.10	TSL:5 MANE Select	c.26_32dupGGGCCGG	p.Ala12GlyfsTer20	frameshift	Exon 2 of 11	ENSP00000339712.4	H3BPZ0
	FBXL19	ENST00000562319.7	TSL:2	c.86_92dupGGGCCGG	p.Ala32GlyfsTer20	frameshift	Exon 2 of 11	ENSP00000455529.2	Q6PCT2-1
	FBXL19	ENST00000565690.5	TSL:5	c.26_32dupGGGCCGG	p.Ala12GlyfsTer20	frameshift	Exon 1 of 9	ENSP00000454344.1	H3BME1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000150 AC: 2 AN: 1331922 Hom.: 0 Cov.: 30 AF XY: 0.00000305 AC XY: 2 AN XY: 655200

African (AFR) AF: 0.00 AC: 0 AN: 27090

American (AMR) AF: 0.00 AC: 0 AN: 22386

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21924

East Asian (EAS) AF: 0.00 AC: 0 AN: 32050

South Asian (SAS) AF: 0.00 AC: 0 AN: 70090

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45022

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3964

European-Non Finnish (NFE) AF: 0.00000190 AC: 2 AN: 1054478

Other (OTH) AF: 0.00 AC: 0 AN: 54918

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	Neurodevelopmental delay (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		4.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2055582969; hg19: chr16-30937088;