10-121479394-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000141.5(FGFR2):c.*463A>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 0.0000423 in 330,756 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000141.5 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FGFR2 | ENST00000358487 | c.*463A>G | 3_prime_UTR_variant | Exon 18 of 18 | 1 | NM_000141.5 | ENSP00000351276.6 | |||
FGFR2 | ENST00000457416 | c.*463A>G | 3_prime_UTR_variant | Exon 18 of 18 | 1 | ENSP00000410294.2 | ||||
FGFR2 | ENST00000613048 | c.*463A>G | 3_prime_UTR_variant | Exon 17 of 17 | 5 | ENSP00000484154.1 | ||||
FGFR2 | ENST00000369061 | c.*463A>G | 3_prime_UTR_variant | Exon 15 of 15 | 1 | ENSP00000358057.4 | ||||
FGFR2 | ENST00000478859 | c.*463A>G | 3_prime_UTR_variant | Exon 17 of 17 | 1 | ENSP00000474011.1 | ||||
FGFR2 | ENST00000604236.5 | n.*1976A>G | non_coding_transcript_exon_variant | Exon 17 of 17 | 1 | ENSP00000474109.1 | ||||
FGFR2 | ENST00000604236.5 | n.*1976A>G | 3_prime_UTR_variant | Exon 17 of 17 | 1 | ENSP00000474109.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152120Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000560 AC: 10AN: 178518Hom.: 0 Cov.: 3 AF XY: 0.0000550 AC XY: 5AN XY: 90968
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152238Hom.: 1 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74450
ClinVar
Submissions by phenotype
Crouzon syndrome Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Beare-Stevenson cutis gyrata syndrome Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Isolated Coronal Synostosis Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Craniosynostosis syndrome Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Saethre-Chotzen syndrome Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at