17-57979243-T-TTGTTGTTGC
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 0P and 3B. BP3BP6_Moderate
The NM_007146.3(VEZF1):c.1046_1047insGCAACAACA(p.Gln347_Gln349dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000152 in 1,446,338 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. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. Q349Q) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 28)
Exomes 𝑓: 0.000015 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
VEZF1
NM_007146.3 disruptive_inframe_insertion
NM_007146.3 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.405
Publications
0 publications found
Genes affected
VEZF1 (HGNC:12949): (vascular endothelial zinc finger 1) Transcriptional regulatory proteins containing tandemly repeated zinc finger domains are thought to be involved in both normal and abnormal cellular proliferation and differentiation. ZNF161 is a C2H2-type zinc finger protein (Koyano-Nakagawa et al., 1994 [PubMed 8035792]). See MIM 603971 for general information on zinc finger proteins.[supplied by OMIM, Sep 2008]
VEZF1 Gene-Disease associations (from GenCC):
- autism spectrum disorderInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
- cardiomyopathy, dilated, 100Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
- dilated cardiomyopathyInheritance: AD Classification: NO_KNOWN Submitted by: ClinGen
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_007146.3
BP6
Variant 17-57979243-T-TTGTTGTTGC is Benign according to our data. Variant chr17-57979243-T-TTGTTGTTGC is described in ClinVar as Benign. ClinVar VariationId is 1686373.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_007146.3. 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 |
|---|---|---|---|---|---|---|---|---|---|
| VEZF1 | NM_007146.3 | MANE Select | c.1046_1047insGCAACAACA | p.Gln347_Gln349dup | disruptive_inframe_insertion | Exon 5 of 6 | NP_009077.2 | Q14119 | |
| VEZF1 | NM_001330393.2 | c.1019_1020insGCAACAACA | p.Gln338_Gln340dup | disruptive_inframe_insertion | Exon 6 of 7 | NP_001317322.1 | J3QSH4 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| VEZF1 | ENST00000581208.2 | TSL:1 MANE Select | c.1046_1047insGCAACAACA | p.Gln347_Gln349dup | disruptive_inframe_insertion | Exon 5 of 6 | ENSP00000462337.1 | Q14119 | |
| VEZF1 | ENST00000258963.7 | TSL:1 | c.500_501insGCAACAACA | p.Gln165_Gln167dup | disruptive_inframe_insertion | Exon 4 of 5 | ENSP00000258963.3 | J9JIC7 | |
| VEZF1 | ENST00000905172.1 | c.1187_1188insGCAACAACA | p.Gln394_Gln396dup | disruptive_inframe_insertion | Exon 6 of 7 | ENSP00000575231.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
28
GnomAD4 exome AF: 0.0000152 AC: 22AN: 1446338Hom.: 0 Cov.: 32 AF XY: 0.0000167 AC XY: 12AN XY: 719530 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
22
AN:
1446338
Hom.:
Cov.:
32
AF XY:
AC XY:
12
AN XY:
719530
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:
32928
American (AMR)
AF:
AC:
3
AN:
44326
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25812
East Asian (EAS)
AF:
AC:
0
AN:
39308
South Asian (SAS)
AF:
AC:
10
AN:
84800
European-Finnish (FIN)
AF:
AC:
0
AN:
52620
Middle Eastern (MID)
AF:
AC:
0
AN:
5636
European-Non Finnish (NFE)
AF:
AC:
7
AN:
1101242
Other (OTH)
AF:
AC:
2
AN:
59666
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.00000000000643774), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.375
Heterozygous variant carriers
0
1
3
4
6
7
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 0.00 AC: 0AN: 150758Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 73666
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
150758
Hom.:
Cov.:
28
AF XY:
AC XY:
0
AN XY:
73666
African (AFR)
AF:
AC:
0
AN:
40900
American (AMR)
AF:
AC:
0
AN:
15142
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3446
East Asian (EAS)
AF:
AC:
0
AN:
5162
South Asian (SAS)
AF:
AC:
0
AN:
4752
European-Finnish (FIN)
AF:
AC:
0
AN:
10432
Middle Eastern (MID)
AF:
AC:
0
AN:
292
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67636
Other (OTH)
AF:
AC:
0
AN:
2086
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not specified (1)
Computational 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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