chr1-179882532-G-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS1
The NM_015602.4(TOR1AIP1):c.30G>T(p.Ala10=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000627 in 1,467,184 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 (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000068 ( 3 hom. )
Consequence
TOR1AIP1
NM_015602.4 synonymous
NM_015602.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.393
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 1-179882532-G-T is Benign according to our data. Variant chr1-179882532-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 737055.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.393 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.0000684 (90/1314934) while in subpopulation SAS AF= 0.00118 (76/64232). AF 95% confidence interval is 0.000969. There are 3 homozygotes in gnomad4_exome. There are 73 alleles in male gnomad4_exome subpopulation. Median coverage is 29. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TOR1AIP1 | NM_015602.4 | c.30G>T | p.Ala10= | synonymous_variant | 1/10 | ENST00000606911.7 | |
TOR1AIP1 | NM_001267578.2 | c.30G>T | p.Ala10= | synonymous_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TOR1AIP1 | ENST00000606911.7 | c.30G>T | p.Ala10= | synonymous_variant | 1/10 | 1 | NM_015602.4 | P4 | |
ENST00000610272.1 | n.64C>A | non_coding_transcript_exon_variant | 1/1 | ||||||
TOR1AIP1 | ENST00000271583.7 | c.30G>T | p.Ala10= | synonymous_variant | 1/11 | 5 | A2 | ||
TOR1AIP1 | ENST00000528443.6 | c.30G>T | p.Ala10= | synonymous_variant | 1/10 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152132Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000111 AC: 11AN: 99120Hom.: 0 AF XY: 0.000175 AC XY: 9AN XY: 51554
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GnomAD4 exome AF: 0.0000684 AC: 90AN: 1314934Hom.: 3 Cov.: 29 AF XY: 0.000114 AC XY: 73AN XY: 640186
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Autosomal recessive limb-girdle muscular dystrophy type 2Y Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 08, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at