GeneBe

rs57786397

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3

The NM_007146.3(VEZF1):​c.1014_1046delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA​(p.Gln339_Gln349del) variant causes a disruptive inframe deletion change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 28)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

VEZF1
NM_007146.3 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.35
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP3
Nonframeshift variant in repetitive region in NM_007146.3

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
VEZF1NM_007146.3 linkc.1014_1046delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA p.Gln339_Gln349del disruptive_inframe_deletion 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.1014_1046delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA p.Gln339_Gln349del disruptive_inframe_deletion Exon 5 of 6 1 NM_007146.3 ENSP00000462337.1 Q14119
VEZF1ENST00000258963.7 linkc.468_500delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA p.Gln157_Gln167del disruptive_inframe_deletion Exon 4 of 5 1 ENSP00000258963.3 J9JIC7
VEZF1ENST00000584396.5 linkc.987_1019delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA p.Gln330_Gln340del disruptive_inframe_deletion Exon 5 of 6 5 ENSP00000464687.1 J3QSH4

Frequencies

GnomAD3 genomes
Cov.:
28
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
6.91e-7
AC:
1
AN:
1446340
Hom.:
0
AF XY:
0.00000139
AC XY:
1
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
Cov.:
28
Bravo
AF:
0.00000378

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