chr17-8173469-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_183065.4(TMEM107):c.*734A>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 0.000127 in 764,380 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.*734A>G | 3_prime_UTR_variant | Exon 5 of 5 | 1 | NM_183065.4 | ENSP00000402732.2 | |||
TMEM107 | ENST00000449985 | c.*783A>G | 3_prime_UTR_variant | Exon 2 of 2 | 1 | ENSP00000404753.2 | ||||
SNORD118 | ENST00000363593.1 | n.119A>G | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152144Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000142 AC: 33AN: 231908Hom.: 0 AF XY: 0.000164 AC XY: 21AN XY: 127946
GnomAD4 exome AF: 0.000140 AC: 86AN: 612236Hom.: 0 Cov.: 0 AF XY: 0.000152 AC XY: 51AN XY: 334680
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152144Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74328
ClinVar
Submissions by phenotype
not provided Uncertain:1
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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 1476725). This variant has not been reported in the literature in individuals affected with SNORD118-related conditions. This variant is present in population databases (rs758890705, gnomAD 0.05%). This variant occurs in the SNORD118 gene, which encodes an RNA molecule that does not result in a protein product. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at