5-142640943-T-G

Variant names:

• chr5-142640943-T-G
• rs12523624
• NM_000800.5:c.-34-26782A>C

Variant summary

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

The NM_000800.5(FGF1):​c.-34-26782A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,794 control chromosomes in the GnomAD database, including 13,580 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 (13580 hom., cov: 32)
• Consequence: FGF1 NM_000800.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGF1	NM_000800.5	c.-34-26782A>C		intron_variant	Intron 1 of 3	ENST00000337706.7	NP_000791.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGF1	ENST00000337706.7	c.-34-26782A>C		intron_variant	Intron 1 of 3	2	NM_000800.5	ENSP00000338548.2

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61941 AN: 151676 Hom.: 13591 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.408 AC: 61924 AN: 151794 Hom.: 13580 Cov.: 32 AF XY: 0.407 AC XY: 30169 AN XY: 74190

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.399

Alfa AF: 0.473 Hom.: 35581

Bravo AF: 0.395

Asia WGS AF: 0.391 AC: 1359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12523624; hg19: chr5-142020508;