NM_004857.3:c.562C>T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004857.3(AKAP5):c.562C>T(p.Arg188Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,614,156 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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. R188Q) has been classified as Benign.
Frequency
Consequence
NM_004857.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AKAP5 | ENST00000394718.4 | c.562C>T | p.Arg188Trp | missense_variant | Exon 2 of 2 | 1 | NM_004857.3 | ENSP00000378207.3 | ||
ZBTB25 | ENST00000555220.5 | c.174-19318G>A | intron_variant | Intron 2 of 2 | 1 | ENSP00000450718.1 | ||||
AKAP5 | ENST00000320636.5 | c.562C>T | p.Arg188Trp | missense_variant | Exon 1 of 1 | 6 | ENSP00000315615.5 | |||
ZBTB25 | ENST00000555424.1 | c.256+18158G>A | intron_variant | Intron 2 of 2 | 5 | ENSP00000451046.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251416Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135904
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461888Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727248
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74448
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.562C>T (p.R188W) alteration is located in exon 2 (coding exon 1) of the AKAP5 gene. This alteration results from a C to T substitution at nucleotide position 562, causing the arginine (R) at amino acid position 188 to be replaced by a tryptophan (W). 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