9-110048735-TCCCCCGGAGTCTCCTGGA-TCCCCCGGAGTCTCCTGGACCCCCGGAGTCTCCTGGA
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM4
The NM_001198656.1(PALM2AKAP2):c.64_81dupTCTCCTGGACCCCCGGAG(p.Ser22_Glu27dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000338 in 1,538,936 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000040 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000033 ( 0 hom. )
Consequence
PALM2AKAP2
NM_001198656.1 conservative_inframe_insertion
NM_001198656.1 conservative_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.690
Publications
1 publications found
Genes affected
PALM2AKAP2 (HGNC:33529): (PALM2 and AKAP2 fusion) This gene belongs to the paralemmin downstream gene (PDG) family defined in PMID:22855693. Paralemmin downstream genes may have evolved contiguously with the paralemmin genes and are associated with other paralemmin paralogs in humans and several other taxa. The gene encodes three distinct protein isoforms, the PALM2 isoform, the AKAP2 isoform and the PALM2-AKAP2 isoform. The biological significance of the PALM2-AKAP2 isoforms is yet unknown. Earlier, PALM2 and AKAP2 were annotated as separate genes and PALM2-AKAP2 was annotated as a readthrough gene. [provided by RefSeq, May 2019]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_001198656.1.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001198656.1. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PALM2AKAP2 | MANE Select | c.582+32724_582+32741dupTCTCCTGGACCCCCGGAG | intron | N/A | NP_009134.1 | Q9Y2D5-4 | |||
| PALM2AKAP2 | c.64_81dupTCTCCTGGACCCCCGGAG | p.Ser22_Glu27dup | conservative_inframe_insertion | Exon 1 of 5 | NP_001185585.1 | Q9Y2D5-7 | |||
| PALM2AKAP2 | c.64_81dupTCTCCTGGACCCCCGGAG | p.Ser22_Glu27dup | conservative_inframe_insertion | Exon 1 of 4 | NP_001004065.2 | Q9Y2D5-5 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PALM2AKAP2 | TSL:1 | c.64_81dupTCTCCTGGACCCCCGGAG | p.Ser22_Glu27dup | conservative_inframe_insertion | Exon 1 of 5 | ENSP00000404782.2 | Q9Y2D5-7 | ||
| PALM2AKAP2 | TSL:1 | c.64_81dupTCTCCTGGACCCCCGGAG | p.Ser22_Glu27dup | conservative_inframe_insertion | Exon 1 of 4 | ENSP00000363649.1 | Q9Y2D5-5 | ||
| PALM2AKAP2 | TSL:2 MANE Select | c.582+32724_582+32741dupTCTCCTGGACCCCCGGAG | intron | N/A | ENSP00000363654.3 | Q9Y2D5-4 |
Frequencies
GnomAD3 genomes 0.0000396 AC: 6AN: 151342Hom.: 0 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
6
AN:
151342
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.0000285 AC: 4AN: 140564 AF XY: 0.0000512 show subpopulations
GnomAD2 exomes
AF:
AC:
4
AN:
140564
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000332 AC: 46AN: 1387594Hom.: 0 Cov.: 31 AF XY: 0.0000408 AC XY: 28AN XY: 686610 show subpopulations
GnomAD4 exome
AF:
AC:
46
AN:
1387594
Hom.:
Cov.:
31
AF XY:
AC XY:
28
AN XY:
686610
show subpopulations
African (AFR)
AF:
AC:
0
AN:
31024
American (AMR)
AF:
AC:
4
AN:
38482
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25042
East Asian (EAS)
AF:
AC:
18
AN:
35874
South Asian (SAS)
AF:
AC:
6
AN:
79688
European-Finnish (FIN)
AF:
AC:
0
AN:
34846
Middle Eastern (MID)
AF:
AC:
0
AN:
4190
European-Non Finnish (NFE)
AF:
AC:
15
AN:
1080614
Other (OTH)
AF:
AC:
3
AN:
57834
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.477
Heterozygous variant carriers
0
3
5
8
10
13
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.0000396 AC: 6AN: 151342Hom.: 0 Cov.: 31 AF XY: 0.0000541 AC XY: 4AN XY: 73926 show subpopulations
GnomAD4 genome
AF:
AC:
6
AN:
151342
Hom.:
Cov.:
31
AF XY:
AC XY:
4
AN XY:
73926
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41256
American (AMR)
AF:
AC:
3
AN:
15208
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3466
East Asian (EAS)
AF:
AC:
0
AN:
5096
South Asian (SAS)
AF:
AC:
1
AN:
4800
European-Finnish (FIN)
AF:
AC:
0
AN:
10578
Middle Eastern (MID)
AF:
AC:
0
AN:
312
European-Non Finnish (NFE)
AF:
AC:
1
AN:
67636
Other (OTH)
AF:
AC:
0
AN:
2080
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.467
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.