7-73671083-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PP3_ModerateBP6
The NM_001077621.2(VPS37D):c.463C>T(p.Arg155Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000168 in 1,611,146 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars). Synonymous variant affecting the same amino acid position (i.e. R155R) has been classified as Likely benign.
Frequency
Consequence
NM_001077621.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VPS37D | NM_001077621.2 | c.463C>T | p.Arg155Cys | missense_variant | Exon 4 of 4 | ENST00000324941.5 | NP_001071089.1 | |
VPS37D | XM_017011779.2 | c.340C>T | p.Arg114Cys | missense_variant | Exon 4 of 4 | XP_016867268.1 | ||
VPS37D | XM_047419927.1 | c.235C>T | p.Arg79Cys | missense_variant | Exon 4 of 4 | XP_047275883.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152192Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000210 AC: 5AN: 238342Hom.: 0 AF XY: 0.0000229 AC XY: 3AN XY: 131174
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1458954Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 725932
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152192Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74346
ClinVar
Submissions by phenotype
EBV-positive nodal T- and NK-cell lymphoma Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at