15-49484458-A-C

Variant names:

• chr15-49484458-A-C
• NM_002009.4:c.539A>C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_002009.4(FGF7):​c.539A>C​(p.Lys180Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000007 in 1,428,756 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.0e-7 (0 hom.)
• Consequence: FGF7 NM_002009.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.36

Genes affected

FGF7 (HGNC:3685): (fibroblast growth factor 7) 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 is a potent epithelial cell-specific growth factor, whose mitogenic activity is predominantly exhibited in keratinocytes but not in fibroblasts and endothelial cells. Studies of mouse and rat homologs of this gene implicated roles in morphogenesis of epithelium, reepithelialization of wounds, hair development and early lung organogenesis. [provided by RefSeq, Jul 2008]

FAM227B (HGNC:26543): (family with sequence similarity 227 member B)

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGF7	NM_002009.4	c.539A>C	p.Lys180Thr	missense_variant	Exon 4 of 4	ENST00000267843.9	NP_002000.1
FAM227B	NM_152647.3	c.1012+23753T>G		intron_variant	Intron 11 of 15	ENST00000299338.11	NP_689860.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGF7	ENST00000267843.9	c.539A>C	p.Lys180Thr	missense_variant	Exon 4 of 4	1	NM_002009.4	ENSP00000267843.4
FAM227B	ENST00000299338.11	c.1012+23753T>G		intron_variant	Intron 11 of 15	2	NM_152647.3	ENSP00000299338.6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.00e-7 AC: 1 AN: 1428756 Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0 AN XY: 711016

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.04e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Dec 28, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.539A>C (p.K180T) alteration is located in exon 4 (coding exon 3) of the FGF7 gene. This alteration results from a A to C substitution at nucleotide position 539, causing the lysine (K) at amino acid position 180 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.36
BayesDel_addAF	Benign	0.010	T
BayesDel_noAF	Benign	-0.22
CADD	Pathogenic	26
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.85	D;D;.
Eigen	Uncertain	0.31
Eigen_PC	Uncertain	0.41
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Benign	0.83	.;T;D
M_CAP	Uncertain	0.25	D
MetaRNN	Uncertain	0.52	D;D;D
MetaSVM	Uncertain	-0.076	T
MutationAssessor	Benign	1.5	L;L;.
PrimateAI	Uncertain	0.54	T
PROVEAN	Uncertain	-3.4	D;.;D
REVEL	Uncertain	0.45
Sift	Uncertain	0.0020	D;.;D
Sift4G	Uncertain	0.0050	D;D;D
Polyphen		0.60	P;P;.
Vest4		0.27
MutPred		0.48		Loss of methylation at K180 (P = 0.0149);Loss of methylation at K180 (P = 0.0149);.;
MVP		0.72
MPC		1.6
ClinPred		0.97	D
GERP RS		5.6
Varity_R		0.55
gMVP		0.86

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr15-49776655;