1-179918249-GA-G
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_015602.4(TOR1AIP1):c.*11del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000708 in 1,412,588 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 7.1e-7 ( 0 hom. )
Consequence
TOR1AIP1
NM_015602.4 3_prime_UTR
NM_015602.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.36
Genes affected
TOR1AIP1 (HGNC:29456): (torsin 1A interacting protein 1) This gene encodes a type 2 integral membrane protein that binds A- and B-type lamins. The encoded protein localizes to the inner nuclear membrane and may be involved in maintaining the attachment of the nuclear membrane to the nuclear lamina during cell division. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Apr 2016]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 1-179918249-GA-G is Benign according to our data. Variant chr1-179918249-GA-G is described in ClinVar as [Likely_benign]. Clinvar id is 257697.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TOR1AIP1 | NM_015602.4 | c.*11del | 3_prime_UTR_variant | 10/10 | ENST00000606911.7 | ||
TOR1AIP1 | NM_001267578.2 | c.*11del | 3_prime_UTR_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TOR1AIP1 | ENST00000606911.7 | c.*11del | 3_prime_UTR_variant | 10/10 | 1 | NM_015602.4 | P4 | ||
TOR1AIP1 | ENST00000435319.8 | c.*11del | 3_prime_UTR_variant | 10/10 | 1 | A2 | |||
TOR1AIP1 | ENST00000271583.7 | c.*11del | 3_prime_UTR_variant | 11/11 | 5 | A2 | |||
TOR1AIP1 | ENST00000528443.6 | c.*11del | 3_prime_UTR_variant | 10/10 | 2 | A2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 7.08e-7 AC: 1AN: 1412588Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 701082
GnomAD4 exome
AF:
AC:
1
AN:
1412588
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
701082
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at