3-48466535-G-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_130384.3(ATRIP):c.*981G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000356 in 1,613,950 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_130384.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATRIP | NM_130384.3 | c.*981G>T | 3_prime_UTR_variant | Exon 13 of 13 | ENST00000320211.10 | NP_569055.1 | ||
TREX1 | NM_033629.6 | c.-26-95G>T | intron_variant | Intron 1 of 1 | ENST00000625293.3 | NP_338599.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152108Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000441 AC: 109AN: 247124Hom.: 2 AF XY: 0.000402 AC XY: 54AN XY: 134364
GnomAD4 exome AF: 0.000373 AC: 545AN: 1461722Hom.: 3 Cov.: 30 AF XY: 0.000380 AC XY: 276AN XY: 727164
GnomAD4 genome AF: 0.000191 AC: 29AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.000255 AC XY: 19AN XY: 74422
ClinVar
Submissions by phenotype
TREX1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at