17-8173466-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_183065.4(TMEM107):c.*737G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000106 in 764,296 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 Uncertain significance (★).
Frequency
Consequence
NM_183065.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM107 | ENST00000437139 | c.*737G>A | 3_prime_UTR_variant | Exon 5 of 5 | 1 | NM_183065.4 | ENSP00000402732.2 | |||
TMEM107 | ENST00000449985 | c.*786G>A | 3_prime_UTR_variant | Exon 2 of 2 | 1 | ENSP00000404753.2 | ||||
SNORD118 | ENST00000363593.1 | n.122G>A | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152168Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000134 AC: 31AN: 231802Hom.: 0 AF XY: 0.000109 AC XY: 14AN XY: 127908
GnomAD4 exome AF: 0.000105 AC: 64AN: 612010Hom.: 0 Cov.: 0 AF XY: 0.000105 AC XY: 35AN XY: 334574
GnomAD4 genome AF: 0.000112 AC: 17AN: 152286Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74482
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant occurs in the SNORD118 gene, which encodes an RNA molecule that does not result in a protein product. This variant is present in population databases (rs201397948, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with SNORD118-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at