15-85639404-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007200.5(AKAP13):c.4192C>T(p.Pro1398Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,612,436 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AKAP13 | NM_007200.5 | c.4192C>T | p.Pro1398Ser | missense_variant | Exon 9 of 37 | ENST00000394518.7 | NP_009131.2 | |
AKAP13 | NM_006738.6 | c.4192C>T | p.Pro1398Ser | missense_variant | Exon 9 of 37 | NP_006729.4 | ||
AKAP13 | NM_001270546.1 | c.112C>T | p.Pro38Ser | missense_variant | Exon 2 of 29 | NP_001257475.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250438Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135368
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1460200Hom.: 0 Cov.: 29 AF XY: 0.00000413 AC XY: 3AN XY: 726476
GnomAD4 genome AF: 0.000105 AC: 16AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74446
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4192C>T (p.P1398S) alteration is located in exon 9 (coding exon 8) of the AKAP13 gene. This alteration results from a C to T substitution at nucleotide position 4192, causing the proline (P) at amino acid position 1398 to be replaced by a serine (S). 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