rs31555

chr5-135935932-A-Cchr5-135935932-A-G

Variant summary

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

The NR_152421.1(FBXL21P):n.403+493A>C 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 0.302 in 152,044 control chromosomes in the GnomAD database, including 7,394 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 0.30 (7394 hom., cov: 32)
• Consequence: FBXL21P NR_152421.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FBXL21P	NR_152421.1	n.403+493A>C		intron_variant, non_coding_transcript_variant
FBXL21P	NR_152420.1	n.399+493A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FBXL21P	ENST00000297158.11	n.83-663A>C		intron_variant, non_coding_transcript_variant
	ENST00000467490.5	n.106-872A>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45869 AN: 151926 Hom.: 7394 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.302 AC: 45882 AN: 152044 Hom.: 7394 Cov.: 32 AF XY: 0.302 AC XY: 22408 AN XY: 74318

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.309

Alfa AF: 0.313 Hom.: 1231

Bravo AF: 0.304

Asia WGS AF: 0.352 AC: 1225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	8.2
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs31555; hg19: chr5-135271621;