7-38726949-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014396.4(VPS41):c.2444G>A(p.Arg815Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000214 in 1,590,708 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014396.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VPS41 | NM_014396.4 | c.2444G>A | p.Arg815Gln | missense_variant | Exon 28 of 29 | ENST00000310301.9 | NP_055211.2 | |
VPS41 | NM_080631.4 | c.2369G>A | p.Arg790Gln | missense_variant | Exon 27 of 28 | NP_542198.2 | ||
VPS41 | XM_017011988.2 | c.1289G>A | p.Arg430Gln | missense_variant | Exon 15 of 16 | XP_016867477.1 | ||
VPS41 | XR_007060008.1 | n.2555G>A | non_coding_transcript_exon_variant | Exon 29 of 29 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152108Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000386 AC: 9AN: 232934Hom.: 0 AF XY: 0.0000474 AC XY: 6AN XY: 126462
GnomAD4 exome AF: 0.0000222 AC: 32AN: 1438482Hom.: 0 Cov.: 30 AF XY: 0.0000252 AC XY: 18AN XY: 715326
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74428
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.2444G>A (p.R815Q) alteration is located in exon 28 (coding exon 28) of the VPS41 gene. This alteration results from a G to A substitution at nucleotide position 2444, causing the arginine (R) at amino acid position 815 to be replaced by a glutamine (Q). 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