3-48447062-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_130384.3(ATRIP):c.217C>T(p.Gln73Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.0000149 in 1,405,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. Q73Q) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_130384.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATRIP | NM_130384.3 | c.217C>T | p.Gln73Ter | stop_gained | 1/13 | ENST00000320211.10 | |
ATRIP-TREX1 | NR_153405.1 | n.284C>T | non_coding_transcript_exon_variant | 1/15 | |||
ATRIP | NM_032166.4 | c.217C>T | p.Gln73Ter | stop_gained | 1/12 | ||
ATRIP | NM_001271022.2 | c.-218+263C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATRIP | ENST00000320211.10 | c.217C>T | p.Gln73Ter | stop_gained | 1/13 | 1 | NM_130384.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000102 AC: 2AN: 196904Hom.: 0 AF XY: 0.0000182 AC XY: 2AN XY: 110158
GnomAD4 exome AF: 0.0000149 AC: 21AN: 1405882Hom.: 0 Cov.: 31 AF XY: 0.0000172 AC XY: 12AN XY: 699046
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2023 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals affected with ATRIP-related conditions. This variant is present in population databases (rs148174212, gnomAD 0.002%). This sequence change creates a premature translational stop signal (p.Gln73*) in the ATRIP gene. It is expected to result in an absent or disrupted protein product. However, the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in ATRIP cause disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at