rs10782001

Variant names:

• chr16-30931304-G-A
• rs10782001
• NM_001382779.1:c.1301+720G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-30931304-G-A
• chr16-30931304-G-C

Variant summary

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

The NM_001382779.1(FBXL19):​c.1301+720G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 151,908 control chromosomes in the GnomAD database, including 24,054 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 0.53 (24054 hom., cov: 32)
• Consequence: FBXL19 NM_001382779.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83
• Publications: 70 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

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.1301+720G>A		intron	N/A	NP_001369708.1	H3BPZ0
	FBXL19	NM_001099784.3		c.1361+720G>A		intron	N/A	NP_001093254.2	Q6PCT2-1
	FBXL19	NM_001382780.1		c.1238+720G>A		intron	N/A	NP_001369709.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FBXL19	ENST00000338343.10	TSL:5 MANE Select	c.1301+720G>A		intron	N/A	ENSP00000339712.4	H3BPZ0
	FBXL19	ENST00000427128.5	TSL:1	c.1034+720G>A		intron	N/A	ENSP00000397913.1	H7C112
	FBXL19	ENST00000562319.7	TSL:2	c.1361+720G>A		intron	N/A	ENSP00000455529.2	Q6PCT2-1

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81038 AN: 151790 Hom.: 24036 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.534 AC: 81101 AN: 151908 Hom.: 24054 Cov.: 32 AF XY: 0.534 AC XY: 39612 AN XY: 74200

African (AFR) AF: 0.276 AC: 11448 AN: 41418

American (AMR) AF: 0.571 AC: 8698 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2398 AN: 3470

East Asian (EAS) AF: 0.905 AC: 4660 AN: 5148

South Asian (SAS) AF: 0.310 AC: 1497 AN: 4828

European-Finnish (FIN) AF: 0.675 AC: 7097 AN: 10510

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43259 AN: 67974

Other (OTH) AF: 0.593 AC: 1253 AN: 2112

Alfa AF: 0.615 Hom.: 95132

Bravo AF: 0.524

Asia WGS AF: 0.546 AC: 1904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0020
DANN	Benign	0.46
PhyloP100		-2.8
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: rs10782001; hg19: chr16-30942625;