7-73669468-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.188C>T(p.Ala63Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000235 in 1,580,478 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 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.188C>T | p.Ala63Val | missense_variant | 2/4 | ENST00000324941.5 | NP_001071089.1 | |
VPS37D | XM_017011779.2 | c.65C>T | p.Ala22Val | missense_variant | 2/4 | XP_016867268.1 | ||
VPS37D | XM_047419927.1 | c.-41C>T | 5_prime_UTR_variant | 2/4 | XP_047275883.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152240Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000576 AC: 11AN: 191072Hom.: 0 AF XY: 0.0000578 AC XY: 6AN XY: 103882
GnomAD4 exome AF: 0.000255 AC: 364AN: 1428238Hom.: 1 Cov.: 31 AF XY: 0.000242 AC XY: 171AN XY: 707640
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152240Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74382
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 18, 2023 | The c.188C>T (p.A63V) 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 188, causing the alanine (A) at amino acid position 63 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