rs3829603

Positions:

• chr17-7443723-A-C

Variant summary

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

The NM_004112.4(FGF11):​c.*577A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 152,206 control chromosomes in the GnomAD database, including 36,586 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 0.69 (36540 hom., cov: 32)
  • Exomes 𝑓: 0.80 (46 hom.)
• Consequence: FGF11 NM_004112.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGF11	NM_004112.4	c.*577A>C		3_prime_UTR_variant	5/5	ENST00000293829.9
FGF11	NM_001303460.2	c.*577A>C		3_prime_UTR_variant	5/5
FGF11	NR_130156.2	n.1295A>C		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGF11	ENST00000293829.9	c.*577A>C		3_prime_UTR_variant	5/5	1	NM_004112.4	P1
FGF11	ENST00000575082.5	c.*577A>C		3_prime_UTR_variant	5/5	2

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104301 AN: 151944 Hom.: 36526 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.697

GnomAD4 exome AF: 0.796 AC: 113 AN: 142 Hom.: 46 Cov.: 0 AF XY: 0.829 AC XY: 63 AN XY: 76

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.750

Gnomad4 FIN exome AF: 0.833

Gnomad4 NFE exome AF: 0.798

Gnomad4 OTH exome AF: 0.700

GnomAD4 genome AF: 0.686 AC: 104362 AN: 152064 Hom.: 36540 Cov.: 32 AF XY: 0.679 AC XY: 50442 AN XY: 74328

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.698

Alfa AF: 0.718 Hom.: 39037

Bravo AF: 0.680

Asia WGS AF: 0.494 AC: 1719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.6
DANN	Benign	0.46
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs3829603; hg19: chr17-7347042; COSMIC: COSV105009389; COSMIC: COSV105009389;