rs339501

chr5-44365531-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004465.2(FGF10):c.325+22827G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.94 in 151,892 control chromosomes in the GnomAD database, including 67,565 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.94 (67565 hom., cov: 30)
• Consequence: FGF10 NM_004465.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGF10	NM_004465.2	c.325+22827G>A		intron_variant		ENST00000264664.5
FGF10	XM_005248264.5	c.325+22827G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGF10	ENST00000264664.5	c.325+22827G>A		intron_variant		1	NM_004465.2	P1

Frequencies

GnomAD3 genomes AF: 0.941 AC: 142770 AN: 151774 Hom.: 67548 Cov.: 30

Gnomad AFR AF: 0.840

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.924

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.987

Gnomad FIN AF: 0.973

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.953

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

GnomAD4 genome AF: 0.940 AC: 142836 AN: 151892 Hom.: 67565 Cov.: 30 AF XY: 0.939 AC XY: 69706 AN XY: 74212

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.924

Gnomad4 ASJ AF: 0.985

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.987

Gnomad4 FIN AF: 0.973

Gnomad4 NFE AF: 0.998

Gnomad4 OTH AF: 0.953

Alfa AF: 0.960 Hom.: 10546

Bravo AF: 0.933

Asia WGS AF: 0.890 AC: 3098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
Cadd	Benign	15
Dann	Benign	0.76

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: rs339501; hg19: chr5-44365633;