5-142638295-C-T

Variant names:

• chr5-142638295-C-T
• rs152528
• NM_000800.5:c.-34-24134G>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.-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
• Publications: 17 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.385 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FGF1	NM_000800.5	MANE Select	c.-34-24134G>A		intron	N/A	NP_000791.1	P05230-1
	FGF1	NM_001144934.2		c.-34-24134G>A		intron	N/A	NP_001138406.1	P05230-1
	FGF1	NM_001144935.2		c.-34-24134G>A		intron	N/A	NP_001138407.1	P05230-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FGF1	ENST00000337706.7	TSL:2 MANE Select	c.-34-24134G>A		intron	N/A	ENSP00000338548.2	P05230-1
	FGF1	ENST00000612258.4	TSL:1	c.-34-24134G>A		intron	N/A	ENSP00000479024.1	P05230-1
	FGF1	ENST00000621536.4	TSL:1	c.-34-24134G>A		intron	N/A	ENSP00000480791.1	P05230-1

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

African (AFR) AF: 0.0983 AC: 4056 AN: 41272

American (AMR) AF: 0.303 AC: 4619 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1016 AN: 3470

East Asian (EAS) AF: 0.225 AC: 1168 AN: 5180

South Asian (SAS) AF: 0.285 AC: 1376 AN: 4828

European-Finnish (FIN) AF: 0.299 AC: 3160 AN: 10576

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26414 AN: 67980

Other (OTH) AF: 0.273 AC: 577 AN: 2110

Alfa AF: 0.348 Hom.: 30616

Bravo AF: 0.274

Asia WGS AF: 0.233 AC: 812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.90
DANN	Benign	0.69
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs152528; hg19: chr5-142017860;