NM_000141.5:c.1974A>G

Variant names:

• chr10-121488003-T-C
• NM_000141.5:c.1974A>G

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_000141.5(FGFR2):​c.1974A>G​(p.Lys658Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: FGFR2 NM_000141.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.967

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 Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BP7: Synonymous conserved (PhyloP=0.967 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FGFR2	NM_000141.5	c.1974A>G	p.Lys658Lys	synonymous_variant	Exon 14 of 18	ENST00000358487.10	NP_000132.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGFR2	ENST00000358487.10	c.1974A>G	p.Lys658Lys	synonymous_variant	Exon 14 of 18	1	NM_000141.5	ENSP00000351276.6
FGFR2	ENST00000457416.7	c.1977A>G	p.Lys659Lys	synonymous_variant	Exon 14 of 18	1		ENSP00000410294.2
FGFR2	ENST00000369056.5	c.1977A>G	p.Lys659Lys	synonymous_variant	Exon 13 of 17	1		ENSP00000358052.1
FGFR2	ENST00000369058.7	c.1977A>G	p.Lys659Lys	synonymous_variant	Exon 14 of 17	1		ENSP00000358054.3
FGFR2	ENST00000613048.4	c.1707A>G	p.Lys569Lys	synonymous_variant	Exon 13 of 17	5		ENSP00000484154.1
FGFR2	ENST00000369061.8	c.1638A>G	p.Lys546Lys	synonymous_variant	Exon 11 of 15	1		ENSP00000358057.4
FGFR2	ENST00000369059.5	c.1632A>G	p.Lys544Lys	synonymous_variant	Exon 12 of 16	5		ENSP00000358055.1
FGFR2	ENST00000360144.7	c.1710A>G	p.Lys570Lys	synonymous_variant	Exon 13 of 17	2		ENSP00000353262.3
FGFR2	ENST00000478859.5	c.1290A>G	p.Lys430Lys	synonymous_variant	Exon 13 of 17	1		ENSP00000474011.1
FGFR2	ENST00000429361.5	c.750A>G	p.Lys250Lys	synonymous_variant	Exon 6 of 9	5		ENSP00000404219.1
FGFR2	ENST00000604236.5	n.*1021A>G		non_coding_transcript_exon_variant	Exon 13 of 17	1		ENSP00000474109.1
FGFR2	ENST00000604236.5	n.*1021A>G		3_prime_UTR_variant	Exon 13 of 17	1		ENSP00000474109.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	6.2
DANN	Benign	0.60

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: chr10-123247517;