13-21671788-C-CT

Position:

• chr13-21671788-C-CT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_002010.3(FGF9):​c.-117dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.11 (1878 hom., cov: 0)
  • Exomes 𝑓: 0.048 (1795 hom.)
• Consequence: FGF9 NM_002010.3 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.911

Genes affected

FGF9 (HGNC:3687): (fibroblast growth factor 9) 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 protein was isolated as a secreted factor that exhibits a growth-stimulating effect on cultured glial cells. In nervous system, this protein is produced mainly by neurons and may be important for glial cell development. Expression of the mouse homolog of this gene was found to be dependent on Sonic hedgehog (Shh) signaling. Mice lacking the homolog gene displayed a male-to-female sex reversal phenotype, which suggested a role in testicular embryogenesis. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 13-21671788-C-CT is Benign according to our data. Variant chr13-21671788-C-CT is described in ClinVar as [Benign]. Clinvar id is 311415.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGF9	NM_002010.3	c.-117dup		5_prime_UTR_variant	1/3	ENST00000382353.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGF9	ENST00000382353.6	c.-117dup		5_prime_UTR_variant	1/3	1	NM_002010.3	P1

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16548 AN: 151476 Hom.: 1862 Cov.: 0

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0554

Gnomad ASJ AF: 0.0523

Gnomad EAS AF: 0.0197

Gnomad SAS AF: 0.0586

Gnomad FIN AF: 0.0253

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.0405

Gnomad OTH AF: 0.0943

GnomAD4 exome AF: 0.0478 AC: 43459 AN: 908904 Hom.: 1795 Cov.: 13 AF XY: 0.0475 AC XY: 22267 AN XY: 468856

Gnomad4 AFR exome AF: 0.274

Gnomad4 AMR exome AF: 0.0304

Gnomad4 ASJ exome AF: 0.0454

Gnomad4 EAS exome AF: 0.0162

Gnomad4 SAS exome AF: 0.0647

Gnomad4 FIN exome AF: 0.0312

Gnomad4 NFE exome AF: 0.0413

Gnomad4 OTH exome AF: 0.0603

GnomAD4 genome AF: 0.110 AC: 16613 AN: 151592 Hom.: 1878 Cov.: 0 AF XY: 0.107 AC XY: 7944 AN XY: 74064

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.0554

Gnomad4 ASJ AF: 0.0523

Gnomad4 EAS AF: 0.0198

Gnomad4 SAS AF: 0.0588

Gnomad4 FIN AF: 0.0253

Gnomad4 NFE AF: 0.0405

Gnomad4 OTH AF: 0.0928

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Symphalangism-brachydactyly syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

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: rs10624265; hg19: chr13-22245927;