16-89709864-T-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_004913.3(VPS9D1):āc.1301A>Cā(p.Asn434Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000539 in 1,613,410 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_004913.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VPS9D1 | ENST00000389386.8 | c.1301A>C | p.Asn434Thr | missense_variant | Exon 11 of 15 | 1 | NM_004913.3 | ENSP00000374037.3 | ||
VPS9D1 | ENST00000561976.5 | c.1091A>C | p.Asn364Thr | missense_variant | Exon 10 of 14 | 1 | ENSP00000454244.1 | |||
VPS9D1 | ENST00000565023.1 | c.101A>C | p.Asn34Thr | missense_variant | Exon 2 of 6 | 5 | ENSP00000455792.1 |
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000165 AC: 41AN: 248738Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 134972
GnomAD4 exome AF: 0.000575 AC: 840AN: 1461246Hom.: 2 Cov.: 31 AF XY: 0.000538 AC XY: 391AN XY: 726952
GnomAD4 genome AF: 0.000191 AC: 29AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1301A>C (p.N434T) alteration is located in exon 11 (coding exon 11) of the VPS9D1 gene. This alteration results from a A to C substitution at nucleotide position 1301, causing the asparagine (N) at amino acid position 434 to be replaced by a threonine (T). 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