rs115771646
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001369369.1(FOXN1):c.1425G>A(p.Pro475=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00103 in 1,613,958 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P475P) has been classified as Likely benign.
Frequency
Consequence
NM_001369369.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXN1 | NM_001369369.1 | c.1425G>A | p.Pro475= | synonymous_variant | 8/9 | ENST00000579795.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXN1 | ENST00000579795.6 | c.1425G>A | p.Pro475= | synonymous_variant | 8/9 | 1 | NM_001369369.1 | P1 | |
FOXN1 | ENST00000226247.2 | c.1425G>A | p.Pro475= | synonymous_variant | 7/8 | 1 | P1 | ||
RSKR | ENST00000481916.6 | c.*1195+69055C>T | intron_variant, NMD_transcript_variant | 1 | |||||
FOXN1 | ENST00000577936.2 | c.1425G>A | p.Pro475= | synonymous_variant | 8/9 | 4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00541 AC: 824AN: 152178Hom.: 11 Cov.: 33
GnomAD3 exomes AF: 0.00140 AC: 351AN: 249902Hom.: 4 AF XY: 0.00105 AC XY: 142AN XY: 135238
GnomAD4 exome AF: 0.000569 AC: 832AN: 1461662Hom.: 7 Cov.: 35 AF XY: 0.000485 AC XY: 353AN XY: 727146
GnomAD4 genome AF: 0.00546 AC: 831AN: 152296Hom.: 12 Cov.: 33 AF XY: 0.00540 AC XY: 402AN XY: 74460
ClinVar
Submissions by phenotype
T-cell immunodeficiency, congenital alopecia, and nail dystrophy Benign:2
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. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 01, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at