chr8-144423927-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_183057.3(VPS28):c.662C>T(p.Ser221Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,613,138 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_183057.3 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: 0.0000328 AC: 5AN: 152242Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000282 AC: 7AN: 248316Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134832
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1460778Hom.: 0 Cov.: 29 AF XY: 0.0000124 AC XY: 9AN XY: 726696
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152360Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74506
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 13, 2023 | The c.662C>T (p.S221F) alteration is located in exon 9 (coding exon 8) of the VPS28 gene. This alteration results from a C to T substitution at nucleotide position 662, causing the serine (S) at amino acid position 221 to be replaced by a phenylalanine (F). 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