NM_007146.3:c.1041_1042delGC
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 4P and 9B. PVS1_StrongBP6BS1BS2
The NM_007146.3(VEZF1):c.1041_1042delGC(p.Gln348AlafsTer27) variant causes a frameshift change. The variant allele was found at a frequency of 0.00377 in 1,574,920 control chromosomes in the GnomAD database, including 69 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_007146.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VEZF1 | ENST00000581208.2 | c.1041_1042delGC | p.Gln348AlafsTer27 | frameshift_variant | Exon 5 of 6 | 1 | NM_007146.3 | ENSP00000462337.1 | ||
VEZF1 | ENST00000258963.7 | c.495_496delGC | p.Gln166fs | frameshift_variant | Exon 4 of 5 | 1 | ENSP00000258963.3 | |||
VEZF1 | ENST00000584396.5 | c.1014_1015delGC | p.Gln339AlafsTer27 | frameshift_variant | Exon 5 of 6 | 5 | ENSP00000464687.1 |
Frequencies
GnomAD3 genomes AF: 0.00727 AC: 1028AN: 141492Hom.: 10 Cov.: 31
GnomAD3 exomes AF: 0.0000987 AC: 23AN: 233112Hom.: 0 AF XY: 0.0000944 AC XY: 12AN XY: 127112
GnomAD4 exome AF: 0.00342 AC: 4897AN: 1433320Hom.: 56 AF XY: 0.00398 AC XY: 2841AN XY: 713132
GnomAD4 genome AF: 0.00734 AC: 1040AN: 141600Hom.: 13 Cov.: 31 AF XY: 0.00791 AC XY: 549AN XY: 69384
ClinVar
Submissions by phenotype
VEZF1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at