3-48466534-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_130384.3(ATRIP):c.*980G>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 0.000242 in 1,613,834 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_130384.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATRIP | NM_130384.3 | c.*980G>A | 3_prime_UTR_variant | Exon 13 of 13 | ENST00000320211.10 | NP_569055.1 | ||
TREX1 | NM_033629.6 | c.-26-96G>A | intron_variant | Intron 1 of 1 | ENST00000625293.3 | NP_338599.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152110Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000850 AC: 21AN: 247100Hom.: 0 AF XY: 0.0000744 AC XY: 10AN XY: 134358
GnomAD4 exome AF: 0.000245 AC: 358AN: 1461724Hom.: 0 Cov.: 30 AF XY: 0.000238 AC XY: 173AN XY: 727158
GnomAD4 genome AF: 0.000217 AC: 33AN: 152110Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74298
ClinVar
Submissions by phenotype
TREX1-related disorder Uncertain:1
The TREX1 c.44G>A variant is predicted to result in the amino acid substitution p.Arg15Lys. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.021% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/3-48507933-G-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at