5-44305012-T-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_004465.2(FGF10):āc.610A>Gā(p.Met204Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000644 in 1,613,974 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004465.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FGF10 | NM_004465.2 | c.610A>G | p.Met204Val | missense_variant | 3/3 | ENST00000264664.5 | NP_004456.1 | |
FGF10 | XM_005248264.5 | c.610A>G | p.Met204Val | missense_variant | 4/4 | XP_005248321.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FGF10 | ENST00000264664.5 | c.610A>G | p.Met204Val | missense_variant | 3/3 | 1 | NM_004465.2 | ENSP00000264664 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000155 AC: 39AN: 251354Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135838
GnomAD4 exome AF: 0.0000588 AC: 86AN: 1461640Hom.: 1 Cov.: 31 AF XY: 0.0000509 AC XY: 37AN XY: 727124
GnomAD4 genome AF: 0.000118 AC: 18AN: 152334Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74482
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Oct 24, 2022 | In silico analysis supports that this missense variant does not alter protein structure/function; Reported in a patient with a disorder of sexual development who also harbored a variant in the SRY gene (Wang et al., 2018); This variant is associated with the following publications: (PMID: 29582157, 32140723) - |
Congenital absence of salivary gland Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | 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