rs3783613
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001078.4(VCAM1):c.1238G>A(p.Gly413Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,612,714 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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. G413A) has been classified as Likely benign.
Frequency
Consequence
NM_001078.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VCAM1 | NM_001078.4 | c.1238G>A | p.Gly413Asp | missense_variant | 6/9 | ENST00000294728.7 | |
VCAM1 | NM_001199834.2 | c.1052G>A | p.Gly351Asp | missense_variant | 6/9 | ||
VCAM1 | NM_080682.3 | c.962G>A | p.Gly321Asp | missense_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VCAM1 | ENST00000294728.7 | c.1238G>A | p.Gly413Asp | missense_variant | 6/9 | 1 | NM_001078.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250124Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135168
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1460634Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726540
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74280
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at