5-44303658-T-C

Position:

• chr5-44303658-T-C

Variant summary

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

The NM_004465.2(FGF10):​c.*1337A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 152,020 control chromosomes in the GnomAD database, including 17,369 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 0.45 (17369 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: FGF10 NM_004465.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.447

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=-0.49).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGF10	NM_004465.2	c.*1337A>G		3_prime_UTR_variant	3/3	ENST00000264664.5	NP_004456.1
FGF10	XM_005248264.5	c.*1337A>G		3_prime_UTR_variant	4/4		XP_005248321.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF10	ENST00000264664	c.*1337A>G		3_prime_UTR_variant	3/3	1	NM_004465.2	ENSP00000264664.4

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68611 AN: 151900 Hom.: 17326 Cov.: 32

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.426

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 FIN exome AF: 0.500

GnomAD4 genome AF: 0.452 AC: 68712 AN: 152018 Hom.: 17369 Cov.: 32 AF XY: 0.450 AC XY: 33412 AN XY: 74312

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.432

Alfa AF: 0.346 Hom.: 9515

Bravo AF: 0.479

Asia WGS AF: 0.525 AC: 1825 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	9.3
DANN	Benign	0.87

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: rs1374961; hg19: chr5-44303760;