chr19-40235151-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001626.6(AKT2):c.1264-4G>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 0.000031 in 1,613,800 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 Likely benign (★).
Frequency
Consequence
NM_001626.6 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 |
---|---|---|---|---|---|---|---|
AKT2 | NM_001626.6 | c.1264-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000392038.7 | |||
AKT2 | NM_001243027.3 | c.1078-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
AKT2 | NM_001243028.3 | c.1078-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
AKT2 | NM_001330511.1 | c.1135-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKT2 | ENST00000392038.7 | c.1264-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001626.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151954Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251376Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135904
GnomAD4 exome AF: 0.0000328 AC: 48AN: 1461846Hom.: 0 Cov.: 31 AF XY: 0.0000371 AC XY: 27AN XY: 727224
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151954Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74210
ClinVar
Submissions by phenotype
Type 2 diabetes mellitus;C3278384:Hypoinsulinemic hypoglycemia and body hemihypertrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 12, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at