5-44305002-T-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_004465.2(FGF10):āc.620A>Cā(p.His207Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00172 in 1,613,888 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_004465.2 missense
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.620A>C | p.His207Pro | missense_variant | Exon 3 of 3 | ENST00000264664.5 | NP_004456.1 | |
FGF10 | XM_005248264.5 | c.620A>C | p.His207Pro | missense_variant | Exon 4 of 4 | XP_005248321.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00140 AC: 213AN: 152206Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00161 AC: 405AN: 251312Hom.: 2 AF XY: 0.00158 AC XY: 215AN XY: 135822
GnomAD4 exome AF: 0.00176 AC: 2567AN: 1461564Hom.: 4 Cov.: 31 AF XY: 0.00167 AC XY: 1214AN XY: 727086
GnomAD4 genome AF: 0.00140 AC: 213AN: 152324Hom.: 1 Cov.: 33 AF XY: 0.00138 AC XY: 103AN XY: 74478
ClinVar
Submissions by phenotype
not specified Benign:1
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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. -
FGF10-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Congenital absence of salivary gland;C0265269:Levy-Hollister syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at