chr4-106324979-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001142416.2(AIMP1):c.-25-6C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 1,585,592 control chromosomes in the GnomAD database, including 25,421 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001142416.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AIMP1 | NM_001142416.2 | c.-25-6C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000672341.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AIMP1 | ENST00000672341.1 | c.-25-6C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_001142416.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.168 AC: 25465AN: 151516Hom.: 2185 Cov.: 32
GnomAD3 exomes AF: 0.173 AC: 40414AN: 233740Hom.: 3622 AF XY: 0.177 AC XY: 22452AN XY: 126578
GnomAD4 exome AF: 0.177 AC: 253564AN: 1433958Hom.: 23237 Cov.: 30 AF XY: 0.179 AC XY: 127166AN XY: 711966
GnomAD4 genome ? AF: 0.168 AC: 25474AN: 151634Hom.: 2184 Cov.: 32 AF XY: 0.169 AC XY: 12554AN XY: 74076
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at