chr14-64468908-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004857.3(AKAP5):c.514C>A(p.Gln172Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,846 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q172R) has been classified as Uncertain significance.
Frequency
Consequence
NM_004857.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AKAP5 | ENST00000394718.4 | c.514C>A | p.Gln172Lys | missense_variant | Exon 2 of 2 | 1 | NM_004857.3 | ENSP00000378207.3 | ||
ZBTB25 | ENST00000555220.5 | c.174-19270G>T | intron_variant | Intron 2 of 2 | 1 | ENSP00000450718.1 | ||||
AKAP5 | ENST00000320636.5 | c.514C>A | p.Gln172Lys | missense_variant | Exon 1 of 1 | 6 | ENSP00000315615.5 | |||
ZBTB25 | ENST00000555424.1 | c.256+18206G>T | intron_variant | Intron 2 of 2 | 5 | ENSP00000451046.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461846Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727218
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.514C>A (p.Q172K) alteration is located in exon 2 (coding exon 1) of the AKAP5 gene. This alteration results from a C to A substitution at nucleotide position 514, causing the glutamine (Q) at amino acid position 172 to be replaced by a lysine (K). 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
Publications
No publications associated with this variant yet.