chr6-151349146-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005100.4(AKAP12):c.755T>C(p.Ile252Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,030 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005100.4 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 |
---|---|---|---|---|---|---|---|
AKAP12 | NM_005100.4 | c.755T>C | p.Ile252Thr | missense_variant | 4/5 | ENST00000402676.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKAP12 | ENST00000402676.7 | c.755T>C | p.Ile252Thr | missense_variant | 4/5 | 5 | NM_005100.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000661 AC: 1AN: 151378Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249926Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135426
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461652Hom.: 0 Cov.: 73 AF XY: 0.00 AC XY: 0AN XY: 727114
GnomAD4 genome ? AF: 0.00000661 AC: 1AN: 151378Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73820
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 15, 2021 | The c.755T>C (p.I252T) alteration is located in exon 4 (coding exon 3) of the AKAP12 gene. This alteration results from a T to C substitution at nucleotide position 755, causing the isoleucine (I) at amino acid position 252 to be replaced by a threonine (T). 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