3-192653613-A-G

Position:

• chr3-192653613-A-G

Variant summary

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

The NM_004113.6(FGF12):​c.13+73568T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,040 control chromosomes in the GnomAD database, including 25,163 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 0.57 (25163 hom., cov: 33)
• Consequence: FGF12 NM_004113.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGF12	NM_004113.6	c.13+73568T>C		intron_variant		ENST00000445105.7	NP_004104.3
FGF12	NM_001377293.1	c.-60+73871T>C		intron_variant			NP_001364222.1
FGF12	NM_001377292.1	c.13+73568T>C		intron_variant			NP_001364221.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF12	ENST00000445105.7	c.13+73568T>C		intron_variant		1	NM_004113.6	ENSP00000393686.1

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86705 AN: 151922 Hom.: 25153 Cov.: 33

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.571 AC: 86744 AN: 152040 Hom.: 25163 Cov.: 33 AF XY: 0.571 AC XY: 42440 AN XY: 74308

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.593

Gnomad4 OTH AF: 0.585

Alfa AF: 0.567 Hom.: 3754

Bravo AF: 0.560

Asia WGS AF: 0.610 AC: 2119 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2886785; hg19: chr3-192371402;