7-5308872-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6
The NM_001080495.3(TNRC18):c.8700+3A>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000504 in 478,224 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001080495.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNRC18 | ENST00000430969.6 | c.8700+3A>C | splice_region_variant, intron_variant | Intron 29 of 29 | 5 | NM_001080495.3 | ENSP00000395538.1 | |||
TNRC18 | ENST00000399537.8 | c.8700+3A>C | splice_region_variant, intron_variant | Intron 29 of 29 | 5 | ENSP00000382452.4 |
Frequencies
GnomAD3 genomes AF: 0.000522 AC: 27AN: 51762Hom.: 0 Cov.: 0
GnomAD3 exomes AF: 0.000279 AC: 52AN: 186310Hom.: 0 AF XY: 0.000303 AC XY: 31AN XY: 102182
GnomAD4 exome AF: 0.000502 AC: 214AN: 426438Hom.: 0 Cov.: 28 AF XY: 0.000538 AC XY: 119AN XY: 221020
GnomAD4 genome AF: 0.000521 AC: 27AN: 51786Hom.: 0 Cov.: 0 AF XY: 0.000646 AC XY: 16AN XY: 24778
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at