rs1522268

chr3-192281763-A-Cchr3-192281763-A-Gchr3-192281763-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004113.6(FGF12):c.228+53598T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 151,814 control chromosomes in the GnomAD database, including 11,350 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 0.37 (11350 hom., cov: 31)
• Consequence: FGF12 NM_004113.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.535

Genes affected

FGF12 (HGNC:3668): (fibroblast growth factor 12) 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 growth factor lacks the N-terminal signal sequence present in most of the FGF family members, but it contains clusters of basic residues that have been demonstrated to act as a nuclear localization signal. When transfected into mammalian cells, this protein accumulated in the nucleus, but was not secreted. The specific function of this gene has not yet been determined. [provided by RefSeq, Dec 2019]

FGF12-AS1 (HGNC:40234): (FGF12 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGF12	NM_004113.6	c.228+53598T>G		intron_variant		ENST00000445105.7
FGF12-AS1	NR_046596.1	n.363-1034A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGF12	ENST00000445105.7	c.228+53598T>G		intron_variant		1	NM_004113.6	A1
FGF12-AS1	ENST00000414920.2	n.363-1034A>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55828 AN: 151698 Hom.: 11336 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.368 AC: 55882 AN: 151814 Hom.: 11350 Cov.: 31 AF XY: 0.377 AC XY: 28011 AN XY: 74204

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.898

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.361

Alfa AF: 0.191 Hom.: 375

Bravo AF: 0.380

Asia WGS AF: 0.672 AC: 2335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	7.4
Dann	Benign	0.81

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: rs1522268; hg19: chr3-191999552;