chr5-61332354-AGCG-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3
The ENST00000252744.6(ZSWIM6):c.98_100delGCG(p.Gly33del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000767 in 1,003,512 control chromosomes in the GnomAD database, with no homozygous occurrence. There is a variant allele frequency bias in the population database for this variant (GnomAdExome4), which may indicate mosaicism or somatic mutations in the reference population data. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000014 ( 0 hom., cov: 29)
Exomes 𝑓: 0.000087 ( 0 hom. )
Consequence
ZSWIM6
ENST00000252744.6 disruptive_inframe_deletion
ENST00000252744.6 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.00
Publications
3 publications found
Genes affected
ZSWIM6 (HGNC:29316): (zinc finger SWIM-type containing 6) The protein encoded by this gene contains a zinc finger SWI2/SNF2 and MuDR (SWIM) domain. Proteins with SWIM domains have been found in a diverse number of species and are predicted to interact with DNA or proteins. Mutations in this gene result in acromelic frontonasal dysostosis. [provided by RefSeq, Apr 2017]
ZSWIM6 Gene-Disease associations (from GenCC):
- acromelic frontonasal dysostosisInheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, PanelApp Australia, Labcorp Genetics (formerly Invitae), G2P
- neurodevelopmental disorder with movement abnormalities, abnormal gait, and autistic featuresInheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
BP3
Nonframeshift variant in repetitive region in ENST00000252744.6
Variant Effect in Transcripts
ACMG analysis was done for transcript: ENST00000252744.6. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ZSWIM6 | NM_020928.2 | MANE Select | c.98_100delGCG | p.Gly33del | disruptive_inframe_deletion | Exon 1 of 14 | NP_065979.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ZSWIM6 | ENST00000252744.6 | TSL:5 MANE Select | c.98_100delGCG | p.Gly33del | disruptive_inframe_deletion | Exon 1 of 14 | ENSP00000252744.5 | ||
| ENSG00000288936 | ENST00000821437.1 | n.-9_-7delCGC | upstream_gene | N/A | |||||
| ENSG00000288936 | ENST00000821446.1 | n.-19_-17delCGC | upstream_gene | N/A |
Frequencies
GnomAD3 genomes 0.0000144 AC: 2AN: 138856Hom.: 0 Cov.: 29 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
138856
Hom.:
Cov.:
29
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: 0.00 AC: 0AN: 302 AF XY: 0.00
GnomAD2 exomes
AF:
AC:
0
AN:
302
AF XY:
Gnomad AMR exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000867 AC: 75AN: 864656Hom.: 0 AF XY: 0.000116 AC XY: 47AN XY: 405430 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
75
AN:
864656
Hom.:
AF XY:
AC XY:
47
AN XY:
405430
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
3
AN:
17438
American (AMR)
AF:
AC:
0
AN:
2842
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
7278
East Asian (EAS)
AF:
AC:
10
AN:
11436
South Asian (SAS)
AF:
AC:
4
AN:
17744
European-Finnish (FIN)
AF:
AC:
3
AN:
6830
Middle Eastern (MID)
AF:
AC:
0
AN:
2040
European-Non Finnish (NFE)
AF:
AC:
49
AN:
768464
Other (OTH)
AF:
AC:
5
AN:
30584
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.288
Heterozygous variant carriers
0
9
19
28
38
47
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 0.0000144 AC: 2AN: 138856Hom.: 0 Cov.: 29 AF XY: 0.0000148 AC XY: 1AN XY: 67684 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
138856
Hom.:
Cov.:
29
AF XY:
AC XY:
1
AN XY:
67684
show subpopulations
African (AFR)
AF:
AC:
0
AN:
38546
American (AMR)
AF:
AC:
1
AN:
14110
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3264
East Asian (EAS)
AF:
AC:
0
AN:
4756
South Asian (SAS)
AF:
AC:
0
AN:
4576
European-Finnish (FIN)
AF:
AC:
0
AN:
8266
Middle Eastern (MID)
AF:
AC:
0
AN:
280
European-Non Finnish (NFE)
AF:
AC:
1
AN:
62322
Other (OTH)
AF:
AC:
0
AN:
1888
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
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
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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