rs11717284

Positions:

• chr3-192207411-T-A
• chr3-192207411-T-C
• chr3-192207411-T-G

Variant summary

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

The NM_004113.6(FGF12):​c.229-36755A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 152,114 control chromosomes in the GnomAD database, including 23,390 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 0.53 (23390 hom., cov: 32)
• Consequence: FGF12 NM_004113.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530

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]

LOC124906320 (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 = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGF12	NM_004113.6	c.229-36755A>T		intron_variant		ENST00000445105.7	NP_004104.3
LOC124906320	XR_007096221.1	n.24024A>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF12	ENST00000445105.7	c.229-36755A>T		intron_variant		1	NM_004113.6	ENSP00000393686	A1

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80542 AN: 151996 Hom.: 23342 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.530 AC: 80647 AN: 152114 Hom.: 23390 Cov.: 32 AF XY: 0.536 AC XY: 39861 AN XY: 74356

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.501

Alfa AF: 0.456 Hom.: 2132

Bravo AF: 0.548

Asia WGS AF: 0.785 AC: 2727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.2
DANN	Benign	0.34

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: rs11717284; hg19: chr3-191925200;