chr20-56384330-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_198437.3(AURKA):c.320-6A>G 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 0.000336 in 1,587,602 control chromosomes in the GnomAD database, including 8 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 Likely benign (★).
Frequency
Consequence
NM_198437.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AURKA | NM_198437.3 | c.320-6A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000395915.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AURKA | ENST00000395915.8 | c.320-6A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_198437.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000881 AC: 22AN: 249786Hom.: 0 AF XY: 0.0000887 AC XY: 12AN XY: 135270
GnomAD4 exome AF: 0.000356 AC: 511AN: 1435308Hom.: 8 Cov.: 29 AF XY: 0.000337 AC XY: 241AN XY: 715612
GnomAD4 genome AF: 0.000151 AC: 23AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74470
ClinVar
Submissions by phenotype
AURKA-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 18, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at