chr17-8173426-A-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_183065.4(TMEM107):c.*777T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000431 in 754,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_183065.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM107 | ENST00000437139 | c.*777T>G | 3_prime_UTR_variant | Exon 5 of 5 | 1 | NM_183065.4 | ENSP00000402732.2 | |||
TMEM107 | ENST00000449985 | c.*826T>G | 3_prime_UTR_variant | Exon 2 of 2 | 1 | ENSP00000404753.2 | ||||
SNORD118 | ENST00000363593.1 | n.*28T>G | downstream_gene_variant | 6 |
Frequencies
GnomAD3 genomes AF: 0.00139 AC: 211AN: 151832Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000338 AC: 78AN: 230514Hom.: 0 AF XY: 0.000228 AC XY: 29AN XY: 127278
GnomAD4 exome AF: 0.000189 AC: 114AN: 602942Hom.: 0 Cov.: 0 AF XY: 0.000161 AC XY: 53AN XY: 329682
GnomAD4 genome AF: 0.00139 AC: 211AN: 151950Hom.: 0 Cov.: 33 AF XY: 0.00151 AC XY: 112AN XY: 74312
ClinVar
Submissions by phenotype
TMEM107-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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at