rs34011

Variant names:

• chr5-142615512-G-A
• rs34011
• NM_000800.5:c.-34-1351C>T

Variant summary

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

The NM_000800.5(FGF1):​c.-34-1351C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,106 control chromosomes in the GnomAD database, including 6,824 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 0.30 (6824 hom., cov: 33)
• Consequence: FGF1 NM_000800.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGF1	NM_000800.5	c.-34-1351C>T		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.-34-1351C>T		intron_variant	Intron 1 of 3	2	NM_000800.5	ENSP00000338548.2

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45098 AN: 151988 Hom.: 6812 Cov.: 33

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.297 AC: 45134 AN: 152106 Hom.: 6824 Cov.: 33 AF XY: 0.297 AC XY: 22089 AN XY: 74342

African (AFR) AF: 0.275 AC: 11395 AN: 41488

American (AMR) AF: 0.209 AC: 3196 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1047 AN: 3472

East Asian (EAS) AF: 0.310 AC: 1601 AN: 5172

South Asian (SAS) AF: 0.349 AC: 1679 AN: 4816

European-Finnish (FIN) AF: 0.339 AC: 3579 AN: 10564

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21774 AN: 67982

Other (OTH) AF: 0.299 AC: 632 AN: 2114

Alfa AF: 0.315 Hom.: 989

Bravo AF: 0.280

Asia WGS AF: 0.304 AC: 1058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.52
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

Publications

LitVar

Other links and lift over

dbSNP: rs34011; hg19: chr5-141995077;