rs1482672

Positions:

• chr5-44362667-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+25691G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 151,314 control chromosomes in the GnomAD database, including 23,759 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 0.54 (23759 hom., cov: 31)
• Consequence: FGF10 NM_004465.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGF10	NM_004465.2	c.325+25691G>A		intron_variant		ENST00000264664.5	NP_004456.1
FGF10	XM_005248264.5	c.325+25691G>A		intron_variant			XP_005248321.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF10	ENST00000264664.5	c.325+25691G>A		intron_variant		1	NM_004465.2	ENSP00000264664.4

Frequencies

GnomAD3 genomes AF: 0.536 AC: 80997 AN: 151196 Hom.: 23760 Cov.: 31

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.535 AC: 81009 AN: 151314 Hom.: 23759 Cov.: 31 AF XY: 0.538 AC XY: 39735 AN XY: 73892

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.555

Alfa AF: 0.601 Hom.: 8614

Bravo AF: 0.508

Asia WGS AF: 0.467 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.0
DANN	Benign	0.51

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: rs1482672; hg19: chr5-44362769; COSMIC: COSV52935510;