17-19939808-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_007202.4(AKAP10):c.1227G>C(p.Trp409Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,878 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. W409L) has been classified as Uncertain significance.
Frequency
Consequence
NM_007202.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AKAP10 | NM_007202.4 | c.1227G>C | p.Trp409Cys | missense_variant | 8/15 | ENST00000225737.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKAP10 | ENST00000225737.11 | c.1227G>C | p.Trp409Cys | missense_variant | 8/15 | 1 | NM_007202.4 | P1 | |
AKAP10 | ENST00000395536.7 | c.1227G>C | p.Trp409Cys | missense_variant | 8/14 | 5 | |||
AKAP10 | ENST00000460046.2 | c.*17G>C | 3_prime_UTR_variant, NMD_transcript_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251084Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135708
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461720Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727152
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2022 | The c.1227G>C (p.W409C) alteration is located in exon 8 (coding exon 8) of the AKAP10 gene. This alteration results from a G to C substitution at nucleotide position 1227, causing the tryptophan (W) at amino acid position 409 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at