7-5308317-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001080495.3(TNRC18):c.8701-5C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00013 in 1,605,948 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001080495.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNRC18 | ENST00000430969.6 | c.8701-5C>T | splice_region_variant, intron_variant | Intron 29 of 29 | 5 | NM_001080495.3 | ENSP00000395538.1 | |||
TNRC18 | ENST00000399537.8 | c.8701-5C>T | splice_region_variant, intron_variant | Intron 29 of 29 | 5 | ENSP00000382452.4 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 151736Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000214 AC: 49AN: 228514Hom.: 0 AF XY: 0.000193 AC XY: 24AN XY: 124342
GnomAD4 exome AF: 0.000129 AC: 187AN: 1454094Hom.: 1 Cov.: 33 AF XY: 0.000129 AC XY: 93AN XY: 722660
GnomAD4 genome AF: 0.000138 AC: 21AN: 151854Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74180
ClinVar
Submissions by phenotype
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at