19-5909024-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001017921.4(VMAC):c.392C>T(p.Pro131Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000454 in 1,584,758 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001017921.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000210 AC: 32AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000727 AC: 14AN: 192686Hom.: 0 AF XY: 0.0000379 AC XY: 4AN XY: 105536
GnomAD4 exome AF: 0.0000279 AC: 40AN: 1432456Hom.: 0 Cov.: 31 AF XY: 0.0000253 AC XY: 18AN XY: 710780
GnomAD4 genome AF: 0.000210 AC: 32AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2021 | The c.392C>T (p.P131L) alteration is located in exon 2 (coding exon 2) of the VMAC gene. This alteration results from a C to T substitution at nucleotide position 392, causing the proline (P) at amino acid position 131 to be replaced by a leucine (L). 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