rs17502618
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152415.3(VPS37A):c.616A>G(p.Ile206Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,613,990 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I206F) has been classified as Benign.
Frequency
Consequence
NM_152415.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS37A | NM_152415.3 | c.616A>G | p.Ile206Val | missense_variant | 5/12 | ENST00000324849.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS37A | ENST00000324849.9 | c.616A>G | p.Ile206Val | missense_variant | 5/12 | 1 | NM_152415.3 | P1 | |
VPS37A | ENST00000521829.5 | c.541A>G | p.Ile181Val | missense_variant | 4/11 | 1 | |||
VPS37A | ENST00000520140.5 | c.616A>G | p.Ile206Val | missense_variant, NMD_transcript_variant | 5/12 | 5 | |||
VPS37A | ENST00000425020.6 | c.*86A>G | 3_prime_UTR_variant, NMD_transcript_variant | 6/12 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251350Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135840
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461828Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727216
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74336
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at