rs1554928978

Positions:

• chr10-121517424-GAACCTCAATCTCTTTGTCCGTGGTGTTAACACCGGCGGCCTAGAAAACAAGGGAAGCAAAAGAAAAGGCTAGACGACACAGGAATGATTGTGGAGGGGGCTGTGGAACCACAAGGCGTCGCACCGGGGGCTTCAGGGGGTGCTGGCCACTGGGAGATTCCGACTGCAGCCCATCCACAAAGCCCACAACCGAGAGACACGGAGC-G

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The ENST00000358487.10(FGFR2):​c.940-165_978del variant causes a splice acceptor, coding sequence, intron change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: FGFR2 ENST00000358487.10 splice_acceptor, coding_sequence, intron
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 9.26

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 Pathogenic. Variant got 12 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 10-121517424-GAACCTCAATCTCTTTGTCCGTGGTGTTAACACCGGCGGCCTAGAAAACAAGGGAAGCAAAAGAAAAGGCTAGACGACACAGGAATGATTGTGGAGGGGGCTGTGGAACCACAAGGCGTCGCACCGGGGGCTTCAGGGGGTGCTGGCCACTGGGAGATTCCGACTGCAGCCCATCCACAAAGCCCACAACCGAGAGACACGGAGC-G is Pathogenic according to our data. Variant chr10-121517424-GAACCTCAATCTCTTTGTCCGTGGTGTTAACACCGGCGGCCTAGAAAACAAGGGAAGCAAAAGAAAAGGCTAGACGACACAGGAATGATTGTGGAGGGGGCTGTGGAACCACAAGGCGTCGCACCGGGGGCTTCAGGGGGTGCTGGCCACTGGGAGATTCCGACTGCAGCCCATCCACAAAGCCCACAACCGAGAGACACGGAGC-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 520630.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGFR2	NM_000141.5	c.940-165_978del		splice_acceptor_variant, coding_sequence_variant, intron_variant	8/18	ENST00000358487.10	NP_000132.3
FGFR2	NM_022970.4	c.1087+1054_1087+1257del		intron_variant		ENST00000457416.7	NP_075259.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGFR2	ENST00000358487.10	c.940-165_978del		splice_acceptor_variant, coding_sequence_variant, intron_variant	8/18	1	NM_000141.5	ENSP00000351276	A2
FGFR2	ENST00000457416.7	c.1087+1054_1087+1257del		intron_variant		1	NM_022970.4	ENSP00000410294	P4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Inborn genetic diseases Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 03, 2015

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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: rs1554928978; hg19: chr10-123276938;