chr13-21671788-C-CTT

Position:

• chr13-21671788-C-CTT

Variant summary

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

The NM_002010.3(FGF9):​c.-118_-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 0.31 (8570 hom., cov: 0)
  • Exomes 𝑓: 0.34 (50112 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-CTT is Benign according to our data. Variant chr13-21671788-C-CTT is described in ClinVar as [Benign]. Clinvar id is 311416.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGF9	NM_002010.3	c.-118_-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.-118_-117dup		5_prime_UTR_variant	1/3	1	NM_002010.3	P1

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46276 AN: 151444 Hom.: 8575 Cov.: 0

Gnomad AFR AF: 0.0766

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.311

GnomAD4 exome AF: 0.343 AC: 311357 AN: 908188 Hom.: 50112 Cov.: 13 AF XY: 0.344 AC XY: 161039 AN XY: 468510

Gnomad4 AFR exome AF: 0.0635

Gnomad4 AMR exome AF: 0.330

Gnomad4 ASJ exome AF: 0.329

Gnomad4 EAS exome AF: 0.371

Gnomad4 SAS exome AF: 0.319

Gnomad4 FIN exome AF: 0.395

Gnomad4 NFE exome AF: 0.352

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.305 AC: 46264 AN: 151560 Hom.: 8570 Cov.: 0 AF XY: 0.307 AC XY: 22757 AN XY: 74052

Gnomad4 AFR AF: 0.0764

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.310

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

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;