rs1219648
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000141(FGFR2):c.109+7033T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151932 control chromosomes in the gnomAD Genomes database, including 12679 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.41 ( 12679 hom., cov: 33)
Consequence
FGFR2
NM_000141 intron
NM_000141 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.442
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
?
Variant 10:121586676-A>G is Benign according to our data. Variant chr10-121586676-A-G is described in ClinVar as [Benign]. Clinvar id is 1663397. Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGFR2 | NM_000141.5 | c.109+7033T>C | intron_variant | ENST00000358487.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGFR2 | ENST00000358487.10 | c.109+7033T>C | intron_variant | 1 | NM_000141.5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.408 AC: 62043AN: 151932Hom.: 12679 Cov.: 33
GnomAD3 genomes
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33
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
FGFR2-related craniosynostosis Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 01, 2022 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out SpliceAI and Pangolin per-transcript scores at