14-96398118-CAGAGGA-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM4BS2
The NM_152327.5(AK7):c.165_170delGGAAGA(p.Glu55_Glu56del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000031 in 1,613,986 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152327.5 disruptive_inframe_deletion
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 |
---|---|---|---|---|---|---|---|---|---|---|
AK7 | ENST00000267584.9 | c.165_170delGGAAGA | p.Glu55_Glu56del | disruptive_inframe_deletion | Exon 2 of 18 | 1 | NM_152327.5 | ENSP00000267584.4 | ||
AK7 | ENST00000555570.1 | c.165_170delGGAAGA | p.Glu55_Glu56del | disruptive_inframe_deletion | Exon 2 of 2 | 2 | ENSP00000451068.1 | |||
AK7 | ENST00000556643.1 | n.176_181delGGAAGA | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000994 AC: 25AN: 251412Hom.: 2 AF XY: 0.000147 AC XY: 20AN XY: 135884
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461832Hom.: 2 AF XY: 0.0000426 AC XY: 31AN XY: 727226
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74314
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant, c.165_170del, results in the deletion of 2 amino acid(s) of the AK7 protein (p.Glu55_Glu56del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs779453953, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with AK7-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at