rs31549

Positions:

• chr5-135940360-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• 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]

(HGNC:):

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]

ACMG classification

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: 68215 AN: 151758 Hom.: 15361 Cov.: 33

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.445

GnomAD4 exome AF: 0.396 AC: 22461 AN: 56760 Hom.: 4609 AF XY: 0.398 AC XY: 11540 AN XY: 28968

Gnomad4 AFR exome AF: 0.385

Gnomad4 AMR exome AF: 0.462

Gnomad4 ASJ exome AF: 0.411

Gnomad4 EAS exome AF: 0.471

Gnomad4 SAS exome AF: 0.456

Gnomad4 FIN exome AF: 0.411

Gnomad4 NFE exome AF: 0.384

Gnomad4 OTH exome AF: 0.419

GnomAD4 genome AF: 0.450 AC: 68288 AN: 151878 Hom.: 15377 Cov.: 33 AF XY: 0.450 AC XY: 33434 AN XY: 74220

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.443

Alfa AF: 0.439 Hom.: 15591

Bravo AF: 0.455

Asia WGS AF: 0.492 AC: 1705 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.5
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs31549; hg19: chr5-135276049;