15-85521518-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007200.5(AKAP13):c.124C>T(p.Arg42Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000768 in 1,614,104 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007200.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AKAP13 | NM_007200.5 | c.124C>T | p.Arg42Cys | missense_variant | 3/37 | ENST00000394518.7 | |
AKAP13 | NM_006738.6 | c.124C>T | p.Arg42Cys | missense_variant | 3/37 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKAP13 | ENST00000394518.7 | c.124C>T | p.Arg42Cys | missense_variant | 3/37 | 1 | NM_007200.5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000143 AC: 36AN: 251430Hom.: 0 AF XY: 0.000147 AC XY: 20AN XY: 135886
GnomAD4 exome AF: 0.0000814 AC: 119AN: 1461840Hom.: 0 Cov.: 31 AF XY: 0.000109 AC XY: 79AN XY: 727220
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74442
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 12, 2022 | The c.124C>T (p.R42C) alteration is located in exon 3 (coding exon 2) of the AKAP13 gene. This alteration results from a C to T substitution at nucleotide position 124, causing the arginine (R) at amino acid position 42 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