chr17-57105642-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003488.4(AKAP1):c.178G>A(p.Val60Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00449 in 1,614,038 control chromosomes in the GnomAD database, including 289 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003488.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AKAP1 | NM_003488.4 | c.178G>A | p.Val60Met | missense_variant | 2/11 | ENST00000337714.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKAP1 | ENST00000337714.8 | c.178G>A | p.Val60Met | missense_variant | 2/11 | 1 | NM_003488.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0238 AC: 3615AN: 152050Hom.: 143 Cov.: 32
GnomAD3 exomes AF: 0.00630 AC: 1582AN: 251260Hom.: 65 AF XY: 0.00448 AC XY: 608AN XY: 135812
GnomAD4 exome AF: 0.00247 AC: 3618AN: 1461870Hom.: 145 Cov.: 78 AF XY: 0.00216 AC XY: 1570AN XY: 727236
GnomAD4 genome ? AF: 0.0238 AC: 3623AN: 152168Hom.: 144 Cov.: 32 AF XY: 0.0234 AC XY: 1741AN XY: 74400
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 31, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at