5-44310216-TG-T

Position:

• chr5-44310216-TG-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_004465.2(FGF10):​c.429+210del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00912 in 152,210 control chromosomes in the GnomAD database, including 14 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.0091 (14 hom., cov: 32)
• Consequence: FGF10 NM_004465.2 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.01

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 5-44310216-TG-T is Benign according to our data. Variant chr5-44310216-TG-T is described in ClinVar as [Likely_benign]. Clinvar id is 1201459.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00912 (1388/152210) while in subpopulation NFE AF= 0.0127 (867/68008). AF 95% confidence interval is 0.012. There are 14 homozygotes in gnomad4. There are 681 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 1388 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGF10	NM_004465.2	c.429+210del		intron_variant		ENST00000264664.5	NP_004456.1
FGF10	XM_005248264.5	c.429+210del		intron_variant			XP_005248321.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF10	ENST00000264664.5	c.429+210del		intron_variant		1	NM_004465.2	ENSP00000264664	P1

Frequencies

GnomAD3 genomes AF: 0.00913 AC: 1388 AN: 152092 Hom.: 14 Cov.: 32

Gnomad AFR AF: 0.00208

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00492

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.000773

Gnomad SAS AF: 0.00704

Gnomad FIN AF: 0.0283

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0127

Gnomad OTH AF: 0.00720

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00912 AC: 1388 AN: 152210 Hom.: 14 Cov.: 32 AF XY: 0.00915 AC XY: 681 AN XY: 74404

Gnomad4 AFR AF: 0.00207

Gnomad4 AMR AF: 0.00491

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.000775

Gnomad4 SAS AF: 0.00705

Gnomad4 FIN AF: 0.0283

Gnomad4 NFE AF: 0.0127

Gnomad4 OTH AF: 0.00712

Alfa AF: 0.0105 Hom.: 2

Bravo AF: 0.00693

Asia WGS AF: 0.00346 AC: 12 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

Aug 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: rs577957727; hg19: chr5-44310318;