rs4151120

Positions:

• chr17-7438829-T-A
• chr17-7438829-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000575235.5(FGF11):​c.-180+299T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,010 control chromosomes in the GnomAD database, including 8,283 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 0.32 (8283 hom., cov: 32)
• Consequence: FGF11 ENST00000575235.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

Genes affected

FGF11 (HGNC:3667): (fibroblast growth factor 11) 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. The function of this gene has not yet been determined. The expression pattern of the mouse homolog implies a role in nervous system development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGF11	NR_130156.2	n.233+299T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGF11	ENST00000575235.5	c.-180+299T>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48404 AN: 151892 Hom.: 8276 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.319 AC: 48422 AN: 152010 Hom.: 8283 Cov.: 32 AF XY: 0.308 AC XY: 22845 AN XY: 74284

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.325

Alfa AF: 0.325 Hom.: 4812

Bravo AF: 0.321

Asia WGS AF: 0.0670 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	11
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4151120; hg19: chr17-7342148;