10-112668280-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_145206.4(VTI1A):c.490C>T(p.Arg164Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,611,908 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R164H) has been classified as Uncertain significance.
Frequency
Consequence
NM_145206.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VTI1A | ENST00000393077.3 | c.490C>T | p.Arg164Cys | missense_variant | Exon 6 of 8 | 2 | NM_145206.4 | ENSP00000376792.2 | ||
VTI1A | ENST00000432306.5 | c.490C>T | p.Arg164Cys | missense_variant | Exon 6 of 8 | 1 | ENSP00000395017.1 | |||
VTI1A | ENST00000705995.1 | c.511C>T | p.Arg171Cys | missense_variant | Exon 7 of 9 | ENSP00000516199.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151952Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 249902Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135018
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1459956Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 726264
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151952Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74200
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.490C>T (p.R164C) alteration is located in exon 6 (coding exon 6) of the VTI1A gene. This alteration results from a C to T substitution at nucleotide position 490, causing the arginine (R) at amino acid position 164 to be replaced by a cysteine (C). 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