Variant rs17169429 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000467490.5(ENSG00000293402):n.106-15A>G variant causes a splice polypyrimidine tract, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0105 in 1,367,592 control chromosomes in the GnomAD database, including 290 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 0.030 ( 163 hom., cov: 32)

Exomes 𝑓: 0.0080 ( 127 hom. )

Consequence

ENST00000467490.5 splice_polypyrimidine_tract, intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.477

Variant links:

Genes affected

FBXL21P (HGNC:13600): (F-box and leucine rich repeat protein 21, pseudogene) This locus represents a transcribed pseudogene that is related to genes encoding members of the F-box family of proteins. [provided by RefSeq, Nov 2017]

FBXL21P links:

(HGNC:):

links:

LECT2 (HGNC:6550): (leukocyte cell derived chemotaxin 2) This gene encodes a secreted, 16 kDa protein that acts as a chemotactic factor to neutrophils and stimulates the growth of chondrocytes and osteoblasts. This protein has high sequence similarity to the chondromodulin repeat regions of the chicken myb-induced myeloid 1 protein. A polymorphism in this gene may be associated with rheumatoid arthritis. [provided by RefSeq, Jul 2008]

LECT2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.25).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FBXL21P	NR_152421.1 linkuse as main transcript	n.599A>G		non_coding_transcript_exon_variant	4/6
FBXL21P	NR_152420.1 linkuse as main transcript	n.595A>G		non_coding_transcript_exon_variant	4/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FBXL21P	ENST00000297158.11 linkuse as main transcript	n.277A>G		non_coding_transcript_exon_variant	2/5
	ENST00000467490.5 linkuse as main transcript	n.106-15A>G		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.0301

AC:

4577

AN:

152122

Hom.:

162

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0847

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0183

Gnomad ASJ

AF:

0.0118

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.0155

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.00733

Gnomad OTH

AF:

0.0292

GnomAD3 exomes

AF:

0.0123

AC:

3054

AN:

249140

Hom.:

AF XY:

0.0106

AC XY:

1434

AN XY:

135142

show subpopulations

Gnomad AFR exome

AF:

0.0839

Gnomad AMR exome

AF:

0.0107

Gnomad ASJ exome

AF:

0.00954

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00128

Gnomad FIN exome

AF:

0.0157

Gnomad NFE exome

AF:

0.00746

Gnomad OTH exome

AF:

0.0114

GnomAD4 exome

AF:

0.00804

AC:

9768

AN:

1215352

Hom.:

127

Cov.:

AF XY:

0.00759

AC XY:

4574

AN XY:

602312

show subpopulations

Gnomad4 AFR exome

AF:

0.0857

Gnomad4 AMR exome

AF:

0.0112

Gnomad4 ASJ exome

AF:

0.00965

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00127

Gnomad4 FIN exome

AF:

0.0148

Gnomad4 NFE exome

AF:

0.00600

Gnomad4 OTH exome

AF:

0.0107

GnomAD4 genome

AF:

0.0302

AC:

4592

AN:

152240

Hom.:

163

Cov.:

AF XY:

0.0295

AC XY:

2193

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.0848

Gnomad4 AMR

AF:

0.0182

Gnomad4 ASJ

AF:

0.0118

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.0155

Gnomad4 NFE

AF:

0.00734

Gnomad4 OTH

AF:

0.0289

Alfa

AF:

0.0181

Hom.:

Bravo

AF:

0.0334

Asia WGS

AF:

0.00751

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.25

CADD

Benign

0.17

DANN

Benign

0.75

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over