7-73669570-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001077621.2(VPS37D):c.290C>T(p.Ala97Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000144 in 1,592,010 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001077621.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VPS37D | NM_001077621.2 | c.290C>T | p.Ala97Val | missense_variant | 2/4 | ENST00000324941.5 | NP_001071089.1 | |
VPS37D | XM_017011779.2 | c.167C>T | p.Ala56Val | missense_variant | 2/4 | XP_016867268.1 | ||
VPS37D | XM_047419927.1 | c.62C>T | p.Ala21Val | missense_variant | 2/4 | XP_047275883.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VPS37D | ENST00000324941.5 | c.290C>T | p.Ala97Val | missense_variant | 2/4 | 1 | NM_001077621.2 | ENSP00000320416 | P1 | |
VPS37D | ENST00000451519.1 | c.139-1444C>T | intron_variant | 5 | ENSP00000413337 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152220Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.0000125 AC: 18AN: 1439790Hom.: 0 Cov.: 31 AF XY: 0.0000112 AC XY: 8AN XY: 713854
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152220Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2022 | The c.290C>T (p.A97V) alteration is located in exon 2 (coding exon 2) of the VPS37D gene. This alteration results from a C to T substitution at nucleotide position 290, causing the alanine (A) at amino acid position 97 to be replaced by a valine (V). 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