rs3135739

chr10-121552610-C-T

Variant summary

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

The NM_000141.5(FGFR2):c.455-1151G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0907 in 152,200 control chromosomes in the GnomAD database, including 1,637 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 0.091 (1637 hom., cov: 32)
• Consequence: FGFR2 NM_000141.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837

Genes affected

FGFR2 (HGNC:3689): (fibroblast growth factor receptor 2) The protein encoded by this gene is a member of the fibroblast growth factor receptor family, where amino acid sequence is highly conserved between members and throughout evolution. FGFR family members differ from one another in their ligand affinities and tissue distribution. A full-length representative protein consists of an extracellular region, composed of three immunoglobulin-like domains, a single hydrophobic membrane-spanning segment and a cytoplasmic tyrosine kinase domain. The extracellular portion of the protein interacts with fibroblast growth factors, setting in motion a cascade of downstream signals, ultimately influencing mitogenesis and differentiation. This particular family member is a high-affinity receptor for acidic, basic and/or keratinocyte growth factor, depending on the isoform. Mutations in this gene are associated with Crouzon syndrome, Pfeiffer syndrome, Craniosynostosis, Apert syndrome, Jackson-Weiss syndrome, Beare-Stevenson cutis gyrata syndrome, Saethre-Chotzen syndrome, and syndromic craniosynostosis. Multiple alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Jan 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGFR2	NM_000141.5	c.455-1151G>A		intron_variant		ENST00000358487.10
FGFR2	NM_022970.4	c.455-1151G>A		intron_variant		ENST00000457416.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGFR2	ENST00000358487.10	c.455-1151G>A		intron_variant		1	NM_000141.5	A2
FGFR2	ENST00000457416.7	c.455-1151G>A		intron_variant		1	NM_022970.4	P4

Frequencies

GnomAD3 genomes AF: 0.0903 AC: 13733 AN: 152082 Hom.: 1620 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.0850

Gnomad ASJ AF: 0.00605

Gnomad EAS AF: 0.0742

Gnomad SAS AF: 0.00830

Gnomad FIN AF: 0.0302

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00348

Gnomad OTH AF: 0.0722

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

GnomAD4 genome AF: 0.0907 AC: 13797 AN: 152200 Hom.: 1637 Cov.: 32 AF XY: 0.0901 AC XY: 6703 AN XY: 74416

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.0859

Gnomad4 ASJ AF: 0.00605

Gnomad4 EAS AF: 0.0734

Gnomad4 SAS AF: 0.00851

Gnomad4 FIN AF: 0.0302

Gnomad4 NFE AF: 0.00348

Gnomad4 OTH AF: 0.0719

Alfa AF: 0.0288 Hom.: 174

Bravo AF: 0.105

Asia WGS AF: 0.0540 AC: 190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.18
Dann	Benign	0.47

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: rs3135739; hg19: chr10-123312124; COSMIC: COSV60648754;