rs152524

Positions:

• chr5-142612824-A-G
• chr5-142612824-A-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+1135T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,914 control chromosomes in the GnomAD database, including 18,235 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 0.48 (18235 hom., cov: 31)
• Consequence: FGF1 NM_000800.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGF1	NM_000800.5	c.169+1135T>C		intron_variant		ENST00000337706.7	NP_000791.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF1	ENST00000337706.7	c.169+1135T>C		intron_variant		2	NM_000800.5	ENSP00000338548	P1
SPRY4-AS1	ENST00000443800.5	n.356+30910A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72792 AN: 151794 Hom.: 18195 Cov.: 31

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.480 AC: 72880 AN: 151914 Hom.: 18235 Cov.: 31 AF XY: 0.479 AC XY: 35588 AN XY: 74270

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.457

Alfa AF: 0.454 Hom.: 3805

Bravo AF: 0.474

Asia WGS AF: 0.508 AC: 1770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.055
DANN	Benign	0.25

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: rs152524; hg19: chr5-141992389;