chr17-28367362-C-CT
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_000638.4(VTN):c.*6dupA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000171 in 1,574,840 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_000638.4 3_prime_UTR
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 |
---|---|---|---|---|---|---|---|---|---|---|
VTN | ENST00000226218 | c.*6dupA | 3_prime_UTR_variant | Exon 8 of 8 | 1 | NM_000638.4 | ENSP00000226218.4 | |||
ENSG00000273171 | ENST00000555059.2 | c.329+88dupA | intron_variant | Intron 2 of 3 | 4 | ENSP00000452347.3 | ||||
SARM1 | ENST00000379061.8 | n.170+2198dupT | intron_variant | Intron 2 of 10 | 2 | |||||
ENSG00000258924 | ENST00000591482.1 | n.555+6516dupT | intron_variant | Intron 5 of 5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000268 AC: 6AN: 223664Hom.: 0 AF XY: 0.0000246 AC XY: 3AN XY: 121868
GnomAD4 exome AF: 0.0000176 AC: 25AN: 1422652Hom.: 0 Cov.: 29 AF XY: 0.0000170 AC XY: 12AN XY: 704984
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
VTN-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