rs2286461

Positions:

• chr4-15962050-G-A
• chr4-15962050-G-C

Variant summary

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

The NM_031950.4(FGFBP2):​c.*20+388C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,976 control chromosomes in the GnomAD database, including 19,348 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 0.50 (19348 hom., cov: 32)
• Consequence: FGFBP2 NM_031950.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.979

Genes affected

FGFBP2 (HGNC:29451): (fibroblast growth factor binding protein 2) This gene encodes a member of the fibroblast growth factor binding protein family. The encoded protein is a serum protein that is selectively secreted by cytotoxic lymphocytes and may be involved in cytotoxic lymphocyte-mediated immunity. An increase in the amount of gene product may be associated with atopic asthma and mild extrinsic asthma.[provided by RefSeq Staff, Oct 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGFBP2	NM_031950.4	c.*20+388C>T		intron_variant		ENST00000259989.7	NP_114156.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGFBP2	ENST00000259989.7	c.*20+388C>T		intron_variant		1	NM_031950.4	ENSP00000259989.6
FGFBP2	ENST00000509331.1	n.83-1439C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75230 AN: 151858 Hom.: 19340 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.495 AC: 75270 AN: 151976 Hom.: 19348 Cov.: 32 AF XY: 0.501 AC XY: 37199 AN XY: 74266

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.532

Alfa AF: 0.529 Hom.: 28017

Bravo AF: 0.494

Asia WGS AF: 0.577 AC: 2007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.41
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2286461; hg19: chr4-15963673;