chr1-100729373-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001078.4(VCAM1):c.1195G>C(p.Glu399Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00001 in 1,593,642 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001078.4 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 |
---|---|---|---|---|---|---|---|
VCAM1 | NM_001078.4 | c.1195G>C | p.Glu399Gln | missense_variant | 5/9 | ENST00000294728.7 | |
VCAM1 | NM_001199834.2 | c.1009G>C | p.Glu337Gln | missense_variant | 5/9 | ||
VCAM1 | NM_080682.3 | c.929-1825G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VCAM1 | ENST00000294728.7 | c.1195G>C | p.Glu399Gln | missense_variant | 5/9 | 1 | NM_001078.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151156Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000971 AC: 14AN: 1442486Hom.: 0 Cov.: 30 AF XY: 0.0000112 AC XY: 8AN XY: 716680
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151156Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73730
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 12, 2023 | The c.1195G>C (p.E399Q) alteration is located in exon 5 (coding exon 5) of the VCAM1 gene. This alteration results from a G to C substitution at nucleotide position 1195, causing the glutamic acid (E) at amino acid position 399 to be replaced by a glutamine (Q). 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