10-73647531-AG-AGGG
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_001114133.3(SYNPO2L):c.2119_2120dupCC(p.Pro708LeufsTer11) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000253 in 1,580,244 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000014 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
SYNPO2L
NM_001114133.3 frameshift
NM_001114133.3 frameshift
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.23
Publications
0 publications found
Genes affected
SYNPO2L (HGNC:23532): (synaptopodin 2 like) Predicted to enable actin binding activity. Predicted to be involved in several processes, including positive regulation of Rho protein signal transduction; positive regulation of stress fiber assembly; and sarcomere organization. Located in cell junction; cytosol; and nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001114133.3. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SYNPO2L | TSL:1 MANE Select | c.2119_2120dupCC | p.Pro708LeufsTer11 | frameshift | Exon 4 of 4 | ENSP00000378289.2 | Q9H987-1 | ||
| SYNPO2L | TSL:1 | c.1447_1448dupCC | p.Pro484LeufsTer11 | frameshift | Exon 2 of 2 | ENSP00000361964.4 | Q9H987-2 | ||
| SYNPO2L-AS1 | n.9_10dupGG | non_coding_transcript_exon | Exon 1 of 2 |
Frequencies
GnomAD3 genomes 0.0000137 AC: 2AN: 145460Hom.: 0 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
145460
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:
GnomAD4 exome AF: 0.00000139 AC: 2AN: 1434784Hom.: 0 Cov.: 37 AF XY: 0.00 AC XY: 0AN XY: 710496 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
2
AN:
1434784
Hom.:
Cov.:
37
AF XY:
AC XY:
0
AN XY:
710496
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
32712
American (AMR)
AF:
AC:
0
AN:
42632
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24750
East Asian (EAS)
AF:
AC:
0
AN:
39158
South Asian (SAS)
AF:
AC:
0
AN:
83694
European-Finnish (FIN)
AF:
AC:
0
AN:
52526
Middle Eastern (MID)
AF:
AC:
0
AN:
5624
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1094738
Other (OTH)
AF:
AC:
0
AN:
58950
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0000000000983081), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.275
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.0000137 AC: 2AN: 145460Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 70958 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
2
AN:
145460
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
70958
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
2
AN:
39364
American (AMR)
AF:
AC:
0
AN:
14642
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3376
East Asian (EAS)
AF:
AC:
0
AN:
4896
South Asian (SAS)
AF:
AC:
0
AN:
4552
European-Finnish (FIN)
AF:
AC:
0
AN:
10000
Middle Eastern (MID)
AF:
AC:
0
AN:
304
European-Non Finnish (NFE)
AF:
AC:
0
AN:
65442
Other (OTH)
AF:
AC:
0
AN:
2002
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.00000000770867), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.400
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
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
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