chr1-179882657-A-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_015602.4(TOR1AIP1):c.155A>T(p.Gln52Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000141 in 1,584,166 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. Q52Q) has been classified as Likely benign.
Frequency
Consequence
NM_015602.4 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TOR1AIP1 | NM_015602.4 | c.155A>T | p.Gln52Leu | missense_variant | 1/10 | ENST00000606911.7 | |
TOR1AIP1 | NM_001267578.2 | c.155A>T | p.Gln52Leu | missense_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TOR1AIP1 | ENST00000606911.7 | c.155A>T | p.Gln52Leu | missense_variant | 1/10 | 1 | NM_015602.4 | P4 | |
TOR1AIP1 | ENST00000271583.7 | c.155A>T | p.Gln52Leu | missense_variant | 1/11 | 5 | A2 | ||
TOR1AIP1 | ENST00000528443.6 | c.155A>T | p.Gln52Leu | missense_variant | 1/10 | 2 | A2 | ||
TOR1AIP1 | ENST00000435319.8 | upstream_gene_variant | 1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000672 AC: 102AN: 151860Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.000260 AC: 59AN: 226836Hom.: 0 AF XY: 0.000187 AC XY: 23AN XY: 122844
GnomAD4 exome AF: 0.0000852 AC: 122AN: 1432188Hom.: 0 Cov.: 30 AF XY: 0.0000606 AC XY: 43AN XY: 710056
GnomAD4 genome AF: 0.000665 AC: 101AN: 151978Hom.: 1 Cov.: 31 AF XY: 0.000713 AC XY: 53AN XY: 74298
ClinVar
Submissions by phenotype
Autosomal recessive limb-girdle muscular dystrophy type 2Y Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 22, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Apr 10, 2019 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 29, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at