5-44388975-TC-T

Position:

• chr5-44388975-TC-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_004465.2(FGF10):​c.-294delG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0104 in 538,012 control chromosomes in the GnomAD database, including 241 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.027 (189 hom., cov: 31)
  • Exomes 𝑓: 0.0038 (52 hom.)
• Consequence: FGF10 NM_004465.2 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.276

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]

FGF10-AS1 (HGNC:49382): (FGF10 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 5-44388975-TC-T is Benign according to our data. Variant chr5-44388975-TC-T is described in ClinVar as [Benign]. Clinvar id is 1236153.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGF10	NM_004465.2	c.-294delG		5_prime_UTR_variant	1/3	ENST00000264664.5	NP_004456.1
FGF10	XM_005248264.5	c.-294delG		5_prime_UTR_variant	2/4		XP_005248321.1
FGF10-AS1	NR_108034.1	n.182+63delC		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGF10	ENST00000264664.5	c.-294delG		5_prime_UTR_variant	1/3	1	NM_004465.2	ENSP00000264664.4
FGF10-AS1	ENST00000502457.1	n.182+63delC		intron_variant		1
FGF10	ENST00000513107.1	c.-294delG		5_prime_UTR_variant	2/2	4		ENSP00000426406.1

Frequencies

GnomAD3 genomes AF: 0.0271 AC: 4123 AN: 152148 Hom.: 189 Cov.: 31

Gnomad AFR AF: 0.0921

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.0138

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000221

Gnomad OTH AF: 0.0220

GnomAD4 exome AF: 0.00381 AC: 1470 AN: 385746 Hom.: 52 Cov.: 0 AF XY: 0.00313 AC XY: 638 AN XY: 203832

Gnomad4 AFR exome AF: 0.0969

Gnomad4 AMR exome AF: 0.00749

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000339

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000266

Gnomad4 OTH exome AF: 0.00799

GnomAD4 genome AF: 0.0271 AC: 4130 AN: 152266 Hom.: 189 Cov.: 31 AF XY: 0.0269 AC XY: 2006 AN XY: 74466

Gnomad4 AFR AF: 0.0919

Gnomad4 AMR AF: 0.0138

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000221

Gnomad4 OTH AF: 0.0218

Alfa AF: 0.00111 Hom.: 1

Bravo AF: 0.0317

Asia WGS AF: 0.00260 AC: 9 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Apr 30, 2019

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17227522; hg19: chr5-44389077;