5-44305207-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004465.2(FGF10):c.430-15G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 1,607,544 control chromosomes in the GnomAD database, including 35,525 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004465.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FGF10 | NM_004465.2 | c.430-15G>C | intron_variant | Intron 2 of 2 | ENST00000264664.5 | NP_004456.1 | ||
FGF10 | XM_005248264.5 | c.430-15G>C | intron_variant | Intron 3 of 3 | XP_005248321.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.178 AC: 27054AN: 152014Hom.: 2736 Cov.: 32
GnomAD3 exomes AF: 0.226 AC: 56575AN: 250338Hom.: 8042 AF XY: 0.217 AC XY: 29332AN XY: 135298
GnomAD4 exome AF: 0.204 AC: 296225AN: 1455412Hom.: 32783 Cov.: 29 AF XY: 0.202 AC XY: 146385AN XY: 724412
GnomAD4 genome AF: 0.178 AC: 27082AN: 152132Hom.: 2742 Cov.: 32 AF XY: 0.177 AC XY: 13143AN XY: 74376
ClinVar
Submissions by phenotype
not provided Benign:2
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Congenital absence of salivary gland 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