5-135938459-C-T

Position:

• chr5-135938459-C-T

Variant summary

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

The NR_152421.1(FBXL21P):​n.893+912C>T 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 0.769 in 152,092 control chromosomes in the GnomAD database, including 45,868 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 0.77 (45863 hom., cov: 30)
  • Exomes 𝑓: 0.64 (5 hom.)
• Consequence: FBXL21P NR_152421.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FBXL21P	NR_152421.1	n.893+912C>T		intron_variant, non_coding_transcript_variant
FBXL21P	NR_152420.1	n.889+912C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FBXL21P	ENST00000297158.11	n.571+912C>T		intron_variant, non_coding_transcript_variant
	ENST00000467490.5	n.385+912C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116773 AN: 151946 Hom.: 45789 Cov.: 30

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.733

GnomAD4 exome AF: 0.643 AC: 18 AN: 28 Hom.: 5 AF XY: 0.556 AC XY: 10 AN XY: 18

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.583

GnomAD4 genome AF: 0.769 AC: 116904 AN: 152064 Hom.: 45863 Cov.: 30 AF XY: 0.771 AC XY: 57276 AN XY: 74328

Gnomad4 AFR AF: 0.937

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.809

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.737

Alfa AF: 0.679 Hom.: 24050

Bravo AF: 0.780

Asia WGS AF: 0.803 AC: 2791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.59
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs31553; hg19: chr5-135274148;