chr15-85579068-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_007200.5(AKAP13):c.1000G>A(p.Glu334Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00126 in 1,614,142 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_007200.5 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 |
---|---|---|---|---|---|---|---|
AKAP13 | NM_007200.5 | c.1000G>A | p.Glu334Lys | missense_variant | 7/37 | ENST00000394518.7 | |
AKAP13 | NM_006738.6 | c.1000G>A | p.Glu334Lys | missense_variant | 7/37 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKAP13 | ENST00000394518.7 | c.1000G>A | p.Glu334Lys | missense_variant | 7/37 | 1 | NM_007200.5 | A2 | |
ENST00000561409.1 | n.931C>T | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00667 AC: 1014AN: 152134Hom.: 18 Cov.: 32
GnomAD3 exomes AF: 0.00146 AC: 366AN: 251272Hom.: 3 AF XY: 0.00102 AC XY: 139AN XY: 135824
GnomAD4 exome AF: 0.000700 AC: 1024AN: 1461890Hom.: 9 Cov.: 30 AF XY: 0.000615 AC XY: 447AN XY: 727246
GnomAD4 genome ? AF: 0.00666 AC: 1014AN: 152252Hom.: 18 Cov.: 32 AF XY: 0.00692 AC XY: 515AN XY: 74446
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 30, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at