17-8173337-C-T
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_183065.4(TMEM107):c.*866G>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 0.306 in 575,800 control chromosomes in the GnomAD database, including 30,702 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_183065.4 3_prime_UTR
Scores
Clinical Significance
Conservation
Publications
- leukoencephalopathy with calcifications and cystsInheritance: AR Classification: STRONG, MODERATE Submitted by: G2P, PanelApp Australia, Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Benign. The variant received -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM107 | ENST00000437139.7 | c.*866G>A | 3_prime_UTR_variant | Exon 5 of 5 | 1 | NM_183065.4 | ENSP00000402732.2 | |||
TMEM107 | ENST00000449985.6 | c.*915G>A | 3_prime_UTR_variant | Exon 2 of 2 | 1 | ENSP00000404753.2 | ||||
SNORD118 | ENST00000363593.2 | n.*115G>A | downstream_gene_variant | 6 |
Frequencies
GnomAD3 genomes AF: 0.265 AC: 40229AN: 151782Hom.: 6500 Cov.: 33 show subpopulations
GnomAD4 exome AF: 0.321 AC: 135943AN: 423900Hom.: 24205 Cov.: 0 AF XY: 0.319 AC XY: 72467AN XY: 227160 show subpopulations
GnomAD4 genome AF: 0.265 AC: 40218AN: 151900Hom.: 6497 Cov.: 33 AF XY: 0.261 AC XY: 19392AN XY: 74228 show subpopulations
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at