8-66634754-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000310421.5(VCPIP1):c.3416G>A(p.Arg1139Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000177 in 1,614,078 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000310421.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VCPIP1 | NM_025054.5 | c.3416G>A | p.Arg1139Lys | missense_variant | 3/3 | ENST00000310421.5 | NP_079330.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VCPIP1 | ENST00000310421.5 | c.3416G>A | p.Arg1139Lys | missense_variant | 3/3 | 1 | NM_025054.5 | ENSP00000309031.4 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000143 AC: 36AN: 251404Hom.: 0 AF XY: 0.000132 AC XY: 18AN XY: 135866
GnomAD4 exome AF: 0.000185 AC: 271AN: 1461894Hom.: 1 Cov.: 31 AF XY: 0.000208 AC XY: 151AN XY: 727248
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 22, 2023 | The c.3416G>A (p.R1139K) alteration is located in exon 3 (coding exon 3) of the VCPIP1 gene. This alteration results from a G to A substitution at nucleotide position 3416, causing the arginine (R) at amino acid position 1139 to be replaced by a lysine (K). 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