rs980510

Positions:

• chr5-44318430-C-A
• chr5-44318430-C-T

Variant summary

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

The ENST00000264664.5(FGF10):​c.326-7900G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,934 control chromosomes in the GnomAD database, including 13,890 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 0.41 (13890 hom., cov: 32)
• Consequence: FGF10 ENST00000264664.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGF10	NM_004465.2	c.326-7900G>T		intron_variant		ENST00000264664.5	NP_004456.1
FGF10	XM_005248264.5	c.326-7900G>T		intron_variant			XP_005248321.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF10	ENST00000264664.5	c.326-7900G>T		intron_variant		1	NM_004465.2	ENSP00000264664	P1

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62947 AN: 151816 Hom.: 13868 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.415 AC: 63011 AN: 151934 Hom.: 13890 Cov.: 32 AF XY: 0.414 AC XY: 30724 AN XY: 74240

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.412

Alfa AF: 0.307 Hom.: 1933

Bravo AF: 0.436

Asia WGS AF: 0.511 AC: 1777 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.76
DANN	Benign	0.68

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: rs980510; hg19: chr5-44318532;