rs41293763
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000141.5(FGFR2):c.1673-12C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00222 in 1,610,884 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000141.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FGFR2 | ENST00000358487.10 | c.1673-12C>T | intron_variant | Intron 12 of 17 | 1 | NM_000141.5 | ENSP00000351276.6 | |||
FGFR2 | ENST00000457416.7 | c.1676-12C>T | intron_variant | Intron 12 of 17 | 1 | ENSP00000410294.2 | ||||
FGFR2 | ENST00000369056.5 | c.1676-12C>T | intron_variant | Intron 11 of 16 | 1 | ENSP00000358052.1 | ||||
FGFR2 | ENST00000369058.7 | c.1676-12C>T | intron_variant | Intron 12 of 16 | 1 | ENSP00000358054.3 | ||||
FGFR2 | ENST00000613048.4 | c.1406-12C>T | intron_variant | Intron 11 of 16 | 5 | ENSP00000484154.1 | ||||
FGFR2 | ENST00000369061.8 | c.1337-12C>T | intron_variant | Intron 9 of 14 | 1 | ENSP00000358057.4 | ||||
FGFR2 | ENST00000369059.5 | c.1331-12C>T | intron_variant | Intron 10 of 15 | 5 | ENSP00000358055.1 | ||||
FGFR2 | ENST00000360144.7 | c.1409-12C>T | intron_variant | Intron 11 of 16 | 2 | ENSP00000353262.3 | ||||
FGFR2 | ENST00000478859.5 | c.989-12C>T | intron_variant | Intron 11 of 16 | 1 | ENSP00000474011.1 | ||||
FGFR2 | ENST00000429361.5 | c.449-12C>T | intron_variant | Intron 4 of 8 | 5 | ENSP00000404219.1 | ||||
FGFR2 | ENST00000604236.5 | n.*720-12C>T | intron_variant | Intron 11 of 16 | 1 | ENSP00000474109.1 |
Frequencies
GnomAD3 genomes AF: 0.00193 AC: 292AN: 151662Hom.: 2 Cov.: 31
GnomAD3 exomes AF: 0.00227 AC: 569AN: 250560Hom.: 0 AF XY: 0.00238 AC XY: 322AN XY: 135448
GnomAD4 exome AF: 0.00225 AC: 3284AN: 1459132Hom.: 11 Cov.: 32 AF XY: 0.00234 AC XY: 1701AN XY: 725902
GnomAD4 genome AF: 0.00193 AC: 293AN: 151752Hom.: 2 Cov.: 31 AF XY: 0.00180 AC XY: 133AN XY: 74086
ClinVar
Submissions by phenotype
not provided Benign:3
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FGFR2-related craniosynostosis Benign:1
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Crouzon syndrome Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Beare-Stevenson cutis gyrata syndrome Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Isolated Coronal Synostosis Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Craniosynostosis syndrome Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Saethre-Chotzen syndrome Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at