chr5-142644691-T-C

Variant names:

• chr5-142644691-T-C
• rs2070715
• NM_000800.5:c.-34-30530A>G

Variant summary

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

The NM_000800.5(FGF1):​c.-34-30530A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 152,058 control chromosomes in the GnomAD database, including 18,010 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 0.46 (18010 hom., cov: 32)
• Consequence: FGF1 NM_000800.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142
• Publications: 8 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGF1	NM_000800.5	c.-34-30530A>G		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.-34-30530A>G		intron_variant	Intron 1 of 3	2	NM_000800.5	ENSP00000338548.2

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69924 AN: 151940 Hom.: 18018 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.460 AC: 69919 AN: 152058 Hom.: 18010 Cov.: 32 AF XY: 0.456 AC XY: 33872 AN XY: 74298

African (AFR) AF: 0.213 AC: 8821 AN: 41476

American (AMR) AF: 0.484 AC: 7385 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1906 AN: 3466

East Asian (EAS) AF: 0.473 AC: 2453 AN: 5186

South Asian (SAS) AF: 0.507 AC: 2439 AN: 4808

European-Finnish (FIN) AF: 0.496 AC: 5237 AN: 10564

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.589 AC: 40033 AN: 67968

Other (OTH) AF: 0.475 AC: 1003 AN: 2112

Alfa AF: 0.549 Hom.: 47278

Bravo AF: 0.451

Asia WGS AF: 0.472 AC: 1639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.71
PhyloP100		0.14
PromoterAI		-0.0072	Neutral
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: rs2070715; hg19: chr5-142024256;