rs31549
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_152421.1(FBXL21P):n.894-129G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 208,638 control chromosomes in the GnomAD database, including 19,986 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 0.45 ( 15377 hom., cov: 33)
Exomes 𝑓: 0.40 ( 4609 hom. )
Consequence
FBXL21P
NR_152421.1 intron, non_coding_transcript
NR_152421.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0140
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]
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FBXL21P | NR_152421.1 | n.894-129G>A | intron_variant, non_coding_transcript_variant | ||||
FBXL21P | NR_152420.1 | n.890-129G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FBXL21P | ENST00000297158.11 | n.572-129G>A | intron_variant, non_coding_transcript_variant | ||||||
ENST00000467490.5 | n.386-129G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.449 AC: 68215AN: 151758Hom.: 15361 Cov.: 33
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GnomAD4 exome AF: 0.396 AC: 22461AN: 56760Hom.: 4609 AF XY: 0.398 AC XY: 11540AN XY: 28968
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GnomAD4 genome ? AF: 0.450 AC: 68288AN: 151878Hom.: 15377 Cov.: 33 AF XY: 0.450 AC XY: 33434AN XY: 74220
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at