13-21671795-T-TC

Position:

• chr13-21671795-T-TC

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_002010.3(FGF9):​c.-118_-117insC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00178 in 1,171,638 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0044 (3 hom., cov: 33)
  • Exomes 𝑓: 0.0014 (2 hom.)
• Consequence: FGF9 NM_002010.3 5_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.142

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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 13-21671795-T-TC is Benign according to our data. Variant chr13-21671795-T-TC is described in ClinVar as [Likely_benign]. Clinvar id is 311417.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd4 at 672 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGF9	NM_002010.3	c.-118_-117insC		5_prime_UTR_variant	1/3	ENST00000382353.6	NP_002001.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF9	ENST00000382353.6	c.-118_-117insC		5_prime_UTR_variant	1/3	1	NM_002010.3	ENSP00000371790	P1

Frequencies

GnomAD3 genomes AF: 0.00439 AC: 666 AN: 151842 Hom.: 3 Cov.: 33

Gnomad AFR AF: 0.0104

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00990

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.000824

Gnomad OTH AF: 0.00671

GnomAD4 exome AF: 0.00139 AC: 1416 AN: 1019678 Hom.: 2 Cov.: 13 AF XY: 0.00137 AC XY: 716 AN XY: 522130

Gnomad4 AFR exome AF: 0.00974

Gnomad4 AMR exome AF: 0.00527

Gnomad4 ASJ exome AF: 0.00278

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000154

Gnomad4 FIN exome AF: 0.0000991

Gnomad4 NFE exome AF: 0.000968

Gnomad4 OTH exome AF: 0.00334

GnomAD4 genome AF: 0.00442 AC: 672 AN: 151960 Hom.: 3 Cov.: 33 AF XY: 0.00425 AC XY: 316 AN XY: 74282

Gnomad4 AFR AF: 0.0105

Gnomad4 AMR AF: 0.00989

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000824

Gnomad4 OTH AF: 0.00664

Alfa AF: 0.00436 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Symphalangism-brachydactyly syndrome Benign:1

Likely 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: rs1555223896; hg19: chr13-22245934;