10-121479533-T-C
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_000141.5(FGFR2):c.*324A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00501 in 1,476,652 control chromosomes in the GnomAD database, including 30 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 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FGFR2 | ENST00000358487 | c.*324A>G | 3_prime_UTR_variant | Exon 18 of 18 | 1 | NM_000141.5 | ENSP00000351276.6 | |||
FGFR2 | ENST00000457416 | c.*324A>G | 3_prime_UTR_variant | Exon 18 of 18 | 1 | ENSP00000410294.2 | ||||
FGFR2 | ENST00000613048 | c.*324A>G | 3_prime_UTR_variant | Exon 17 of 17 | 5 | ENSP00000484154.1 | ||||
FGFR2 | ENST00000369061 | c.*324A>G | 3_prime_UTR_variant | Exon 15 of 15 | 1 | ENSP00000358057.4 | ||||
FGFR2 | ENST00000478859 | c.*324A>G | 3_prime_UTR_variant | Exon 17 of 17 | 1 | ENSP00000474011.1 | ||||
FGFR2 | ENST00000604236.5 | n.*1837A>G | non_coding_transcript_exon_variant | Exon 17 of 17 | 1 | ENSP00000474109.1 | ||||
FGFR2 | ENST00000604236.5 | n.*1837A>G | 3_prime_UTR_variant | Exon 17 of 17 | 1 | ENSP00000474109.1 |
Frequencies
GnomAD3 genomes AF: 0.00394 AC: 599AN: 152160Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00365 AC: 510AN: 139644Hom.: 4 AF XY: 0.00349 AC XY: 256AN XY: 73436
GnomAD4 exome AF: 0.00513 AC: 6795AN: 1324374Hom.: 28 Cov.: 20 AF XY: 0.00501 AC XY: 3268AN XY: 651740
GnomAD4 genome AF: 0.00394 AC: 600AN: 152278Hom.: 2 Cov.: 33 AF XY: 0.00357 AC XY: 266AN XY: 74458
ClinVar
Submissions by phenotype
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. -
not provided Benign:1
- -
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