chr17-57979243-T-TTGCTGCTGC
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP3BP6BS2
The NM_007146.3(VEZF1):c.1038_1046dupGCAGCAGCA(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 0.00113 in 150,760 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_007146.3 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VEZF1 | ENST00000581208.2 | c.1038_1046dupGCAGCAGCA | p.Gln347_Gln349dup | disruptive_inframe_insertion | Exon 5 of 6 | 1 | NM_007146.3 | ENSP00000462337.1 | ||
VEZF1 | ENST00000258963.7 | c.492_500dupGCAGCAGCA | p.Gln165_Gln167dup | disruptive_inframe_insertion | Exon 4 of 5 | 1 | ENSP00000258963.3 | |||
VEZF1 | ENST00000584396.5 | c.1011_1019dupGCAGCAGCA | p.Gln338_Gln340dup | disruptive_inframe_insertion | Exon 5 of 6 | 5 | ENSP00000464687.1 |
Frequencies
GnomAD3 genomes AF: 0.00114 AC: 171AN: 150648Hom.: 0 Cov.: 28
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00159 AC: 2303AN: 1446168Hom.: 1 Cov.: 32 AF XY: 0.00158 AC XY: 1135AN XY: 719462
GnomAD4 genome AF: 0.00113 AC: 171AN: 150760Hom.: 0 Cov.: 28 AF XY: 0.000977 AC XY: 72AN XY: 73668
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