rs780207480
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_001382430.1(AKT1):c.570C>T(p.Asp190=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,612,936 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001382430.1 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AKT1 | NM_001382430.1 | c.570C>T | p.Asp190= | splice_region_variant, synonymous_variant | 8/15 | ENST00000649815.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKT1 | ENST00000649815.2 | c.570C>T | p.Asp190= | splice_region_variant, synonymous_variant | 8/15 | NM_001382430.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000527 AC: 8AN: 151924Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000440 AC: 11AN: 250236Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135356
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461012Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 726788
GnomAD4 genome ? AF: 0.0000527 AC: 8AN: 151924Hom.: 0 Cov.: 33 AF XY: 0.0000944 AC XY: 7AN XY: 74184
ClinVar
Submissions by phenotype
Cowden syndrome 6 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 15, 2022 | - - |
Benign, criteria provided, single submitter | clinical testing | Mendelics | Aug 22, 2023 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 12, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at