chr5-44305283-TTC-T

Position:

• chr5-44305283-TTC-T

Variant summary

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

The NM_004465.2(FGF10):​c.430-93_430-92del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00927 in 1,210,706 control chromosomes in the GnomAD database, including 458 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.013 (86 hom., cov: 32)
  • Exomes 𝑓: 0.0087 (372 hom.)
• Consequence: FGF10 NM_004465.2 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.750

Genes affected

FGF10 (HGNC:3666): (fibroblast growth factor 10) 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 exhibits mitogenic activity for keratinizing epidermal cells, but essentially no activity for fibroblasts, which is similar to the biological activity of FGF7. Studies of the mouse homolog of suggested that this gene is required for embryonic epidermal morphogenesis including brain development, lung morphogenesis, and initiation of lim bud formation. This gene is also implicated to be a primary factor in the process of wound healing. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 5-44305283-TTC-T is Benign according to our data. Variant chr5-44305283-TTC-T is described in ClinVar as [Likely_benign]. Clinvar id is 1191155.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGF10	NM_004465.2	c.430-93_430-92del		intron_variant		ENST00000264664.5
FGF10	XM_005248264.5	c.430-93_430-92del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGF10	ENST00000264664.5	c.430-93_430-92del		intron_variant		1	NM_004465.2	P1

Frequencies

GnomAD3 genomes AF: 0.0132 AC: 2010 AN: 152168 Hom.: 86 Cov.: 32

Gnomad AFR AF: 0.00166

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0593

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.0124

Gnomad FIN AF: 0.0234

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00123

Gnomad OTH AF: 0.0153

GnomAD4 exome AF: 0.00870 AC: 9210 AN: 1058420 Hom.: 372 AF XY: 0.00834 AC XY: 4533 AN XY: 543412

Gnomad4 AFR exome AF: 0.00160

Gnomad4 AMR exome AF: 0.0554

Gnomad4 ASJ exome AF: 0.0000426

Gnomad4 EAS exome AF: 0.116

Gnomad4 SAS exome AF: 0.00993

Gnomad4 FIN exome AF: 0.0169

Gnomad4 NFE exome AF: 0.000601

Gnomad4 OTH exome AF: 0.0121

GnomAD4 genome AF: 0.0132 AC: 2017 AN: 152286 Hom.: 86 Cov.: 32 AF XY: 0.0165 AC XY: 1226 AN XY: 74462

Gnomad4 AFR AF: 0.00166

Gnomad4 AMR AF: 0.0596

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.0124

Gnomad4 FIN AF: 0.0234

Gnomad4 NFE AF: 0.00123

Gnomad4 OTH AF: 0.0161

Alfa AF: 0.00556 Hom.: 4

Bravo AF: 0.0145

Asia WGS AF: 0.0860 AC: 298 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 06, 2019

- -

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: rs17228248; hg19: chr5-44305385;