rs752171066
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM4_SupportingPP5_Moderate
The NM_183065.4(TMEM107):c.298_300del(p.Phe100del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,613,984 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. F100F) has been classified as Likely benign.
Frequency
Consequence
NM_183065.4 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM107 | NM_183065.4 | c.298_300del | p.Phe100del | inframe_deletion | 4/5 | ENST00000437139.7 | |
LOC105371520 | XR_934201.3 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM107 | ENST00000437139.7 | c.298_300del | p.Phe100del | inframe_deletion | 4/5 | 1 | NM_183065.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251392Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135904
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461882Hom.: 0 AF XY: 0.0000248 AC XY: 18AN XY: 727236
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74296
ClinVar
Submissions by phenotype
Orofaciodigital syndrome 16 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 13, 2017 | - - |
Joubert syndrome 29 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 13, 2017 | - - |
Orofaciodigital syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Department of Genetics, Yale University | Sep 01, 2015 | Initially identified from whole exome sequencing of a patient with orofaciodigital syndrome. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at