X-151396890-G-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001363810.1(VMA21):āc.51G>Cā(p.Glu17Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00089 in 522,449 control chromosomes in the GnomAD database, including 4 homozygotes. There are 119 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 9/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_001363810.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VMA21 | NM_001363810.1 | c.51G>C | p.Glu17Asp | missense_variant | Exon 1 of 3 | NP_001350739.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VMA21 | ENST00000370361.5 | c.51G>C | p.Glu17Asp | missense_variant | Exon 2 of 4 | 5 | ENSP00000359386.1 | |||
ENSG00000287918 | ENST00000660681.2 | n.248C>G | non_coding_transcript_exon_variant | Exon 1 of 2 | ||||||
ENSG00000287918 | ENST00000664935.1 | n.129C>G | non_coding_transcript_exon_variant | Exon 1 of 2 |
Frequencies
GnomAD3 genomes AF: 0.00256 AC: 283AN: 110576Hom.: 3 Cov.: 21 AF XY: 0.00238 AC XY: 78AN XY: 32804
GnomAD3 exomes AF: 0.000507 AC: 52AN: 102574Hom.: 1 AF XY: 0.000348 AC XY: 13AN XY: 37366
GnomAD4 exome AF: 0.000435 AC: 179AN: 411828Hom.: 1 Cov.: 0 AF XY: 0.000263 AC XY: 40AN XY: 151894
GnomAD4 genome AF: 0.00259 AC: 286AN: 110621Hom.: 3 Cov.: 21 AF XY: 0.00240 AC XY: 79AN XY: 32859
ClinVar
Submissions by phenotype
See cases Benign:1
ACMG classification criteria: BS2, BP4 -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at