rs2121875

Positions:

• chr5-44365443-C-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_004465.2(FGF10):​c.325+22915G>T 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 151,194 control chromosomes in the GnomAD database, including 23,722 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.54 (23722 hom., cov: 30)
• Consequence: FGF10 NM_004465.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0450

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BP6: Variant 5-44365443-C-A is Benign according to our data. Variant chr5-44365443-C-A is described in ClinVar as [Benign]. Clinvar id is 1663361.Status of the report is criteria_provided_single_submitter, 1 stars.
• 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	UniProt
FGF10	NM_004465.2	c.325+22915G>T		intron_variant		ENST00000264664.5
FGF10	XM_005248264.5	c.325+22915G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGF10	ENST00000264664.5	c.325+22915G>T		intron_variant		1	NM_004465.2	P1

Frequencies

GnomAD3 genomes AF: 0.535 AC: 80899 AN: 151086 Hom.: 23723 Cov.: 30

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.664

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: 80909 AN: 151194 Hom.: 23722 Cov.: 30 AF XY: 0.537 AC XY: 39664 AN XY: 73828

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.556

Alfa AF: 0.650 Hom.: 59083

Bravo AF: 0.507

Asia WGS AF: 0.467 AC: 1623 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

Invitae

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	11
DANN	Benign	0.62

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: rs2121875; hg19: chr5-44365545;