rs9831045

Variant names:

• chr3-192757470-T-A
• rs9831045
• ENST00000450716.5:c.-131+10234A>T

Your query was ambiguous. Multiple possible variants found:

• chr3-192757470-T-A
• chr3-192757470-T-C

Variant summary

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

The ENST00000450716.5(FGF12):​c.-131+10234A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 152,128 control chromosomes in the GnomAD database, including 35,842 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 0.68 (35842 hom., cov: 32)
• Consequence: FGF12 ENST00000450716.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGF12	ENST00000450716.5	c.-131+10234A>T		intron_variant	Intron 1 of 5	5		ENSP00000397635.1

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102755 AN: 152010 Hom.: 35789 Cov.: 32

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.676 AC: 102873 AN: 152128 Hom.: 35842 Cov.: 32 AF XY: 0.673 AC XY: 50019 AN XY: 74358

Gnomad4 AFR AF: 0.852

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.675

Alfa AF: 0.649 Hom.: 4057

Bravo AF: 0.693

Asia WGS AF: 0.600 AC: 2085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9831045; hg19: chr3-192475259;