rs17217240

chr5-142613829-C-Achr5-142613829-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.169+130G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0236 in 960,512 control chromosomes in the GnomAD database, including 1,533 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 0.065 (850 hom., cov: 33)
  • Exomes 𝑓: 0.016 (683 hom.)
• Consequence: FGF1 NM_000800.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

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]

SPRY4-AS1 (HGNC:53465): (SPRY4 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGF1	NM_000800.5	c.169+130G>T		intron_variant		ENST00000337706.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGF1	ENST00000337706.7	c.169+130G>T		intron_variant		2	NM_000800.5	P1
SPRY4-AS1	ENST00000443800.5	n.356+31915C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0645 AC: 9806 AN: 152128 Hom.: 847 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0295

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.0298

Gnomad FIN AF: 0.00245

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.00484

Gnomad OTH AF: 0.0444

GnomAD4 exome AF: 0.0159 AC: 12824 AN: 808266 Hom.: 683 AF XY: 0.0155 AC XY: 6241 AN XY: 403936

Gnomad4 AFR exome AF: 0.197

Gnomad4 AMR exome AF: 0.0210

Gnomad4 ASJ exome AF: 0.0140

Gnomad4 EAS exome AF: 0.112

Gnomad4 SAS exome AF: 0.0246

Gnomad4 FIN exome AF: 0.00329

Gnomad4 NFE exome AF: 0.00401

Gnomad4 OTH exome AF: 0.0305

GnomAD4 genome AF: 0.0646 AC: 9831 AN: 152246 Hom.: 850 Cov.: 33 AF XY: 0.0637 AC XY: 4740 AN XY: 74460

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.0294

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.0296

Gnomad4 FIN AF: 0.00245

Gnomad4 NFE AF: 0.00485

Gnomad4 OTH AF: 0.0440

Alfa AF: 0.00960 Hom.: 14

Bravo AF: 0.0722

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	1.7
Dann	Benign	0.64

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: rs17217240; hg19: chr5-141993394;