4-15938608-C-A

Variant names:

• chr4-15938608-C-A
• rs12503796
• NM_005130.5:c.-242+79G>T

Variant summary

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

The NM_005130.5(FGFBP1):​c.-242+79G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 152,108 control chromosomes in the GnomAD database, including 13,923 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 (13904 hom., cov: 32)
  • Exomes 𝑓: 0.57 (19 hom.)
• Consequence: FGFBP1 NM_005130.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488

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=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGFBP1	NM_005130.5	c.-242+79G>T		intron_variant	Intron 1 of 2	ENST00000382333.2	NP_005121.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGFBP1	ENST00000382333.2	c.-242+79G>T		intron_variant	Intron 1 of 2	3	NM_005130.5	ENSP00000371770.1

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62637 AN: 151884 Hom.: 13893 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.420

GnomAD4 exome AF: 0.566 AC: 60 AN: 106 Hom.: 19 Cov.: 0 AF XY: 0.532 AC XY: 33 AN XY: 62

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.615

Gnomad4 NFE exome AF: 0.548

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.412 AC: 62664 AN: 152002 Hom.: 13904 Cov.: 32 AF XY: 0.417 AC XY: 30996 AN XY: 74284

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.415

Alfa AF: 0.441 Hom.: 2523

Bravo AF: 0.399

Asia WGS AF: 0.379 AC: 1318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	6.0
DANN	Benign	0.86

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs12503796; hg19: chr4-15940231;