chr5-142638295-C-T

Position:

• chr5-142638295-C-T

Variant summary

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

The NM_000800.5(FGF1):​c.-34-24134G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 151,886 control chromosomes in the GnomAD database, including 7,280 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 0.28 (7280 hom., cov: 32)
• Consequence: FGF1 NM_000800.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

FGF1 (HGNC:3665): (fibroblast growth factor 1) The protein encoded by this gene is a member of the fibroblast growth factor (FGF) family. FGF family members possess broad mitogenic and cell survival activities, and are involved in a variety of biological processes, including embryonic development, cell growth, morphogenesis, tissue repair, tumor growth and invasion. This protein functions as a modifier of endothelial cell migration and proliferation, as well as an angiogenic factor. It acts as a mitogen for a variety of mesoderm- and neuroectoderm-derived cells in vitro, thus is thought to be involved in organogenesis. Multiple alternatively spliced variants encoding different isoforms have been described. [provided by RefSeq, Jan 2009]

FGF1 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGF1	NM_000800.5	c.-34-24134G>A		intron_variant		ENST00000337706.7	NP_000791.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF1	ENST00000337706.7	c.-34-24134G>A		intron_variant		2	NM_000800.5	ENSP00000338548.2

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42857 AN: 151768 Hom.: 7281 Cov.: 32

Gnomad AFR AF: 0.0985

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.282 AC: 42841 AN: 151886 Hom.: 7280 Cov.: 32 AF XY: 0.277 AC XY: 20535 AN XY: 74258

Gnomad4 AFR AF: 0.0983

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.273

Alfa AF: 0.366 Hom.: 23325

Bravo AF: 0.274

Asia WGS AF: 0.233 AC: 812 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	0.90
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs152528; hg19: chr5-142017860;