4-15935377-C-T

Variant names:

• chr4-15935377-C-T
• rs732244
• NM_005130.5:c.*551G>A

Variant summary

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

The NM_005130.5(FGFBP1):​c.*551G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,948 control chromosomes in the GnomAD database, including 13,866 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 0.41 (13866 hom., cov: 32)
• Consequence: FGFBP1 NM_005130.5 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

Genes affected

FGFBP1 (HGNC:19695): (fibroblast growth factor binding protein 1) This gene encodes a secreted fibroblast growth factor carrier protein. The encoded protein plays a critical role in cell proliferation, differentiation and migration by binding to fibroblast growth factors and potentiating their biological effects on target cells. The encoded protein may also play a role in tumor growth as an angiogenic switch molecule, and expression of this gene has been associated with several types of cancer including pancreatic and colorectal adenocarcinoma. A pseudogene of this gene is also located on the short arm of chromosome 4. [provided by RefSeq, Nov 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGFBP1	NM_005130.5	c.*551G>A		downstream_gene_variant		ENST00000382333.2	NP_005121.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGFBP1	ENST00000382333.2	c.*551G>A		downstream_gene_variant		3	NM_005130.5	ENSP00000371770.1

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62513 AN: 151830 Hom.: 13855 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.412 AC: 62540 AN: 151948 Hom.: 13866 Cov.: 32 AF XY: 0.417 AC XY: 30941 AN XY: 74254

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.414

Alfa AF: 0.422 Hom.: 2011

Bravo AF: 0.398

Asia WGS AF: 0.376 AC: 1307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.7
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs732244; hg19: chr4-15937000;