7-73667969-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001077621.2(VPS37D):c.11C>T(p.Ala4Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000078 in 1,063,810 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A4P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001077621.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VPS37D | NM_001077621.2 | c.11C>T | p.Ala4Val | missense_variant | Exon 1 of 4 | ENST00000324941.5 | NP_001071089.1 | |
VPS37D | XM_017011779.2 | c.16-1450C>T | intron_variant | Intron 1 of 3 | XP_016867268.1 | |||
VPS37D | XM_047419927.1 | c.-487C>T | upstream_gene_variant | XP_047275883.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000549 AC: 8AN: 145820Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000450 AC: 1AN: 2220Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 1164
GnomAD4 exome AF: 0.0000817 AC: 75AN: 917990Hom.: 0 Cov.: 28 AF XY: 0.0000856 AC XY: 37AN XY: 432300
GnomAD4 genome AF: 0.0000549 AC: 8AN: 145820Hom.: 0 Cov.: 30 AF XY: 0.0000564 AC XY: 4AN XY: 70972
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.11C>T (p.A4V) alteration is located in exon 1 (coding exon 1) of the VPS37D gene. This alteration results from a C to T substitution at nucleotide position 11, causing the alanine (A) at amino acid position 4 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