NM_017775.4:c.*1589T>C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_017775.4(TTC19):c.*1589T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0326 in 445,342 control chromosomes in the GnomAD database, including 311 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_017775.4 3_prime_UTR
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TTC19 | NM_017775.4 | c.*1589T>C | 3_prime_UTR_variant | Exon 10 of 10 | ENST00000261647.10 | NP_060245.3 | ||
NCOR1 | NM_006311.4 | c.*3185A>G | downstream_gene_variant | ENST00000268712.8 | NP_006302.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0291 AC: 4354AN: 149568Hom.: 91 Cov.: 31
GnomAD3 exomes AF: 0.0290 AC: 3578AN: 123262Hom.: 91 AF XY: 0.0297 AC XY: 2009AN XY: 67548
GnomAD4 exome AF: 0.0343 AC: 10150AN: 295652Hom.: 220 Cov.: 0 AF XY: 0.0333 AC XY: 5611AN XY: 168500
GnomAD4 genome AF: 0.0291 AC: 4352AN: 149690Hom.: 91 Cov.: 31 AF XY: 0.0288 AC XY: 2103AN XY: 73124
ClinVar
Submissions by phenotype
Mitochondrial complex III deficiency nuclear type 2 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at