14-104773098-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_001382430.1(AKT1):c.958-6G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000589 in 1,613,682 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_001382430.1 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AKT1 | NM_001382430.1 | c.958-6G>A | splice_region_variant, intron_variant | ENST00000649815.2 | NP_001369359.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000120 AC: 30AN: 250752Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135570
GnomAD4 exome AF: 0.0000554 AC: 81AN: 1461404Hom.: 0 Cov.: 36 AF XY: 0.0000509 AC XY: 37AN XY: 726990
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152278Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74468
ClinVar
Submissions by phenotype
Cowden syndrome 6 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at