6-132683157-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004666.3(VNN1):āc.1525T>Cā(p.Cys509Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000619 in 1,453,394 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_004666.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VNN1 | NM_004666.3 | c.1525T>C | p.Cys509Arg | missense_variant | 7/7 | ENST00000367928.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VNN1 | ENST00000367928.5 | c.1525T>C | p.Cys509Arg | missense_variant | 7/7 | 1 | NM_004666.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000123 AC: 3AN: 243696Hom.: 0 AF XY: 0.0000152 AC XY: 2AN XY: 131744
GnomAD4 exome AF: 0.00000619 AC: 9AN: 1453394Hom.: 0 Cov.: 30 AF XY: 0.00000969 AC XY: 7AN XY: 722692
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 28, 2022 | The c.1525T>C (p.C509R) alteration is located in exon 7 (coding exon 7) of the VNN1 gene. This alteration results from a T to C substitution at nucleotide position 1525, causing the cysteine (C) at amino acid position 509 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at