NM_000800.5:c.170-595C>A

Variant names:

• chr5-142601400-G-T
• rs34010
• NM_000800.5:c.170-595C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000800.5(FGF1):​c.170-595C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,002 control chromosomes in the GnomAD database, including 5,464 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 0.25 (5464 hom., cov: 31)
• Consequence: FGF1 NM_000800.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000800.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FGF1	NM_000800.5	MANE Select	c.170-595C>A		intron	N/A	NP_000791.1
	FGF1	NM_001144892.3		c.170-595C>A		intron	N/A	NP_001138364.1
	FGF1	NM_001144934.2		c.170-595C>A		intron	N/A	NP_001138406.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FGF1	ENST00000337706.7	TSL:2 MANE Select	c.170-595C>A		intron	N/A	ENSP00000338548.2
	FGF1	ENST00000359370.10	TSL:1	c.170-595C>A		intron	N/A	ENSP00000352329.6
	FGF1	ENST00000612258.4	TSL:1	c.170-595C>A		intron	N/A	ENSP00000479024.1

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38316 AN: 151884 Hom.: 5456 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.252 AC: 38325 AN: 152002 Hom.: 5464 Cov.: 31 AF XY: 0.253 AC XY: 18792 AN XY: 74310

African (AFR) AF: 0.123 AC: 5109 AN: 41478

American (AMR) AF: 0.187 AC: 2848 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 863 AN: 3472

East Asian (EAS) AF: 0.308 AC: 1589 AN: 5154

South Asian (SAS) AF: 0.323 AC: 1555 AN: 4814

European-Finnish (FIN) AF: 0.330 AC: 3475 AN: 10546

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.324 AC: 22031 AN: 67966

Other (OTH) AF: 0.255 AC: 537 AN: 2108

Alfa AF: 0.265 Hom.: 889

Bravo AF: 0.231

Asia WGS AF: 0.285 AC: 990 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.1
DANN	Benign	0.43
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs34010; hg19: chr5-141980965;