16-89710978-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_004913.3(VPS9D1):c.866G>A(p.Arg289Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000034 in 1,442,202 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_004913.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS9D1 | NM_004913.3 | c.866G>A | p.Arg289Lys | missense_variant | 10/15 | ENST00000389386.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS9D1 | ENST00000389386.8 | c.866G>A | p.Arg289Lys | missense_variant | 10/15 | 1 | NM_004913.3 | A2 | |
VPS9D1 | ENST00000561976.5 | c.656G>A | p.Arg219Lys | missense_variant | 9/14 | 1 | P2 | ||
VPS9D1 | ENST00000565452.1 | n.165G>A | non_coding_transcript_exon_variant | 3/3 | 3 | ||||
VPS9D1 | ENST00000568691.5 | n.793G>A | non_coding_transcript_exon_variant | 6/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152164Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000338 AC: 2AN: 59206Hom.: 0 AF XY: 0.0000328 AC XY: 1AN XY: 30516
GnomAD4 exome AF: 0.0000318 AC: 41AN: 1290038Hom.: 0 Cov.: 33 AF XY: 0.0000287 AC XY: 18AN XY: 626314
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152164Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74342
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at