GeneBe

17-57979243-TTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC-TTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC

Variant names:

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2

The NM_007146.3(VEZF1):​c.1023_1046dupGCAGCAGCAGCAGCAGCAGCAGCA​(p.Gln342_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 0.00000501 in 1,597,100 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. Q349Q) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.000046 ( 0 hom., cov: 28)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

VEZF1
NM_007146.3 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.405
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP3
Nonframeshift variant in repetitive region in NM_007146.3
BS2
High AC in GnomAd4 at 7 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
VEZF1NM_007146.3 linkc.1023_1046dupGCAGCAGCAGCAGCAGCAGCAGCA p.Gln342_Gln349dup disruptive_inframe_insertion Exon 5 of 6 ENST00000581208.2 NP_009077.2 Q14119

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
VEZF1ENST00000581208.2 linkc.1023_1046dupGCAGCAGCAGCAGCAGCAGCAGCA p.Gln342_Gln349dup disruptive_inframe_insertion Exon 5 of 6 1 NM_007146.3 ENSP00000462337.1 Q14119
VEZF1ENST00000258963.7 linkc.477_500dupGCAGCAGCAGCAGCAGCAGCAGCA p.Gln160_Gln167dup disruptive_inframe_insertion Exon 4 of 5 1 ENSP00000258963.3 J9JIC7
VEZF1ENST00000584396.5 linkc.996_1019dupGCAGCAGCAGCAGCAGCAGCAGCA p.Gln333_Gln340dup disruptive_inframe_insertion Exon 5 of 6 5 ENSP00000464687.1 J3QSH4

Frequencies

GnomAD3 genomes
AF:
0.0000465
AC:
7
AN:
150648
Hom.:
0
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.000172
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
6.91e-7
AC:
1
AN:
1446340
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
719532
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.08e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000464
AC:
7
AN:
150760
Hom.:
0
Cov.:
28
AF XY:
0.0000407
AC XY:
3
AN XY:
73668
show subpopulations
Gnomad4 AFR
AF:
0.000171
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs57786397; hg19: chr17-56056604; API