rs17217240

Variant names:

• chr5-142613829-C-A
• rs17217240
• NM_000800.5:c.169+130G>T

Your query was ambiguous. Multiple possible variants found:

• chr5-142613829-C-A
• chr5-142613829-C-T

Variant summary

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

The ENST00000337706.7(FGF1):​c.169+130G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0236 in 960,512 control chromosomes in the GnomAD database, including 1,533 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 0.065 (850 hom., cov: 33)
  • Exomes 𝑓: 0.016 (683 hom.)
• Consequence: FGF1 ENST00000337706.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 2 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000337706.7. 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.169+130G>T		intron	N/A	NP_000791.1
	FGF1	NM_001144892.3		c.169+130G>T		intron	N/A	NP_001138364.1
	FGF1	NM_001144934.2		c.169+130G>T		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.169+130G>T		intron	N/A	ENSP00000338548.2
	FGF1	ENST00000359370.10	TSL:1	c.169+130G>T		intron	N/A	ENSP00000352329.6
	FGF1	ENST00000612258.4	TSL:1	c.169+130G>T		intron	N/A	ENSP00000479024.1

Frequencies

GnomAD3 genomes AF: 0.0645 AC: 9806 AN: 152128 Hom.: 847 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0295

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.0298

Gnomad FIN AF: 0.00245

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.00484

Gnomad OTH AF: 0.0444

GnomAD4 exome AF: 0.0159 AC: 12824 AN: 808266 Hom.: 683 AF XY: 0.0155 AC XY: 6241 AN XY: 403936

African (AFR) AF: 0.197 AC: 3740 AN: 18960

American (AMR) AF: 0.0210 AC: 396 AN: 18842

Ashkenazi Jewish (ASJ) AF: 0.0140 AC: 214 AN: 15308

East Asian (EAS) AF: 0.112 AC: 3576 AN: 31858

South Asian (SAS) AF: 0.0246 AC: 1153 AN: 46826

European-Finnish (FIN) AF: 0.00329 AC: 146 AN: 44416

Middle Eastern (MID) AF: 0.0329 AC: 86 AN: 2612

European-Non Finnish (NFE) AF: 0.00401 AC: 2376 AN: 592222

Other (OTH) AF: 0.0305 AC: 1137 AN: 37222

GnomAD4 genome AF: 0.0646 AC: 9831 AN: 152246 Hom.: 850 Cov.: 33 AF XY: 0.0637 AC XY: 4740 AN XY: 74460

African (AFR) AF: 0.193 AC: 8009 AN: 41506

American (AMR) AF: 0.0294 AC: 450 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3470

East Asian (EAS) AF: 0.135 AC: 698 AN: 5182

South Asian (SAS) AF: 0.0296 AC: 143 AN: 4828

European-Finnish (FIN) AF: 0.00245 AC: 26 AN: 10616

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.00485 AC: 330 AN: 68022

Other (OTH) AF: 0.0440 AC: 93 AN: 2116

Alfa AF: 0.0164 Hom.: 33

Bravo AF: 0.0722

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.7
DANN	Benign	0.64
PhyloP100		0.072
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: rs17217240; hg19: chr5-141993394; COSMIC: COSV107427764; COSMIC: COSV107427764;