chr4-83462666-T-TA
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_139076.3(ABRAXAS1):c.1032_1033insT(p.Lys345Ter) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000384 in 1,613,898 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. I344I) has been classified as Likely benign.
Frequency
Consequence
NM_139076.3 frameshift
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 |
---|---|---|---|---|---|---|---|
ABRAXAS1 | NM_139076.3 | c.1032_1033insT | p.Lys345Ter | frameshift_variant | 9/9 | ENST00000321945.12 | |
ABRAXAS1 | NM_001345962.2 | c.705_706insT | p.Lys236Ter | frameshift_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABRAXAS1 | ENST00000321945.12 | c.1032_1033insT | p.Lys345Ter | frameshift_variant | 9/9 | 1 | NM_139076.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152250Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000417 AC: 61AN: 1461648Hom.: 0 Cov.: 33 AF XY: 0.0000536 AC XY: 39AN XY: 727136
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152250Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74394
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jun 24, 2021 | This sequence change inserts 1 nucleotide in exon 9 of the FAM175A mRNA (c.1032dupT), causing a premature translational stop signal in the last exon of the FAM175A mRNA (p.Lys345*). While this is not anticipated to result in nonsense mediated decay, it is expected to result in a truncated FAM175A protein. The current clinical and genetic evidence is not sufficient to establish whether truncating variants in FAM175A cause disease. Therefore, this variant has been classified as a Variant of Uncertain Significance. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a FAM175A-related disease. ClinVar contains an entry for this variant (Variation ID: 128214). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at